preprocessing.ipynb

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      "name": "preprocessing.ipynb",
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      "cell_type": "markdown",
      "metadata": {
        "tags": [],
        "id": "13b7bc53-22f3-4bb0-8778-18bc0d2570e3"
      },
      "source": [
        "# Предобработка данных метилирования генома человека\n",
        "\n",
        "**Эта тетрадка выложена только для ознакомления, код не выполнится поскольку сырые данные не хранятся на этом диске. Но если вы захотите воспроизвести или изменить предобработку, то вы можете скачать эту тетрадку и сырые данные на локальную машину и прописать пути к соответствующим файлам, тогда все будет работать.**\n",
        "\n",
        "## Описание данных\n",
        "\n",
        "Датасет с данными о метилировании ДНК GSE87571 в 476 366 сайтах распо по всему геному белых кровяных телец из когорты населения (N = 421) в возрасте от 14 до 94 лет, количество образцов составляет 732.\n",
        "\n",
        "Адрес датасета на сайте GEO\n",
        "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87571"
      ],
      "id": "13b7bc53-22f3-4bb0-8778-18bc0d2570e3"
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    {
      "cell_type": "code",
      "metadata": {
        "id": "46bca1e4-6f96-441d-adfa-ce224c5969af"
      },
      "source": [
        "import time\n",
        "import sys\n",
        "import numpy as np\n",
        "import pandas as pd\n",
        "\n",
        "import matplotlib.pyplot as plt\n",
        "import plotly.graph_objects as go\n",
        "from plotly.subplots import make_subplots\n",
        "import plotly.figure_factory as ff"
      ],
      "id": "46bca1e4-6f96-441d-adfa-ce224c5969af",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "5e540ebb-848a-4658-9c65-35c8970d22fc"
      },
      "source": [
        "try:\n",
        "    path_main_dir = r\"C:\\Users\\IvanovNikita\"\\\n",
        "                    \n",
        "except:    \n",
        "    raise Exception('Задайте путь к корневой папке с файлами')"
      ],
      "id": "5e540ebb-848a-4658-9c65-35c8970d22fc",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "2add535b-d670-4e71-8aa7-3b9439c7386d"
      },
      "source": [
        "## Загрузка данных с уровнями метилирования в CG-islands"
      ],
      "id": "2add535b-d670-4e71-8aa7-3b9439c7386d"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "2501931d-6f38-460e-acc6-5b0233db23cd"
      },
      "source": [
        "# Загрузим матрицы значений \n",
        "data_1 = pd.read_csv(path_main_dir+'\\\\raw_data\\\\GSE87571_matrix1of2.txt',\n",
        "                     sep='\t')"
      ],
      "id": "2501931d-6f38-460e-acc6-5b0233db23cd",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "d3f615a4-bfe4-42eb-9dc7-5f9c4faf38be"
      },
      "source": [
        "data_2 = pd.read_csv(path_main_dir+'\\\\raw_data\\\\GSE87571_matrix2of2.txt',\n",
        "                     sep='\t')"
      ],
      "id": "d3f615a4-bfe4-42eb-9dc7-5f9c4faf38be",
      "execution_count": null,
      "outputs": []
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      },
      "source": [
        "# Установим в качестве индексов\n",
        "data_2 = data_2.set_index(\n",
        "    'ID_REF',\n",
        "    drop = True)"
      ],
      "id": "d7993f2f-d4bc-427d-86b2-2b54d32c93d4",
      "execution_count": null,
      "outputs": []
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        "data_1 = data_1.set_index(\n",
        "    'ID_REF',\n",
        "    drop = True)"
      ],
      "id": "39476b3c-d1c7-4356-b7d9-9af62b998e5e",
      "execution_count": null,
      "outputs": []
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        "outputId": "dbc33716-4b9f-498e-8a28-793a78b66325"
      },
      "source": [
        "data_joined = data_1.join(data_2, how = 'outer')\n",
        "\n",
        "display(data_joined.shape)\n",
        "display(data_joined.head())\n",
        "display(data_joined.tail())"
      ],
      "id": "2906cb00-eaaa-4ec8-9057-ecbed1a45da8",
      "execution_count": null,
      "outputs": [
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              "                  X1  X1.1  X10     X10.1  X100    X100.1  X101    X101.1  \\\n",
              "ID_REF                                                                      \n",
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              "ID_REF                                             \n",
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              "      <td>0.0</td>\n",
              "      <td>0.112058</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.070752</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.095896</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.056537</td>\n",
              "      <td>0.0</td>\n",
              "      <td>...</td>\n",
              "      <td>0.080128</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.072277</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.070170</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.091591</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.086221</td>\n",
              "      <td>0.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>ch.22.48274842R</th>\n",
              "      <td>0.028080</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.035582</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.023578</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.025565</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.031796</td>\n",
              "      <td>0.0</td>\n",
              "      <td>...</td>\n",
              "      <td>0.034908</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.028587</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.031882</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.032754</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.033597</td>\n",
              "      <td>0.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>5 rows × 1464 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                       X1  X1.1       X10  X10.1      X100  X100.1      X101  \\\n",
              "ID_REF                                                                         \n",
              "ch.22.909671F    0.057891   0.0  0.221108    0.0  0.066405     0.0  0.076406   \n",
              "ch.22.46830341F  0.042315   0.0  0.034829    0.0  0.025640     0.0  0.043598   \n",
              "ch.22.1008279F   0.005898   0.0  0.006287    0.0  0.006652     0.0  0.013686   \n",
              "ch.22.47579720R  0.083398   0.0  0.112058    0.0  0.070752     0.0  0.095896   \n",
              "ch.22.48274842R  0.028080   0.0  0.035582    0.0  0.023578     0.0  0.025565   \n",
              "\n",
              "                 X101.1      X102  X102.1  ...       X95  X95.1       X96  \\\n",
              "ID_REF                                     ...                              \n",
              "ch.22.909671F       0.0  0.044699     0.0  ...  0.115592    0.0  0.054574   \n",
              "ch.22.46830341F     0.0  0.021270     0.0  ...  0.031185    0.0  0.029953   \n",
              "ch.22.1008279F      0.0  0.008111     0.0  ...  0.008182    0.0  0.011095   \n",
              "ch.22.47579720R     0.0  0.056537     0.0  ...  0.080128    0.0  0.072277   \n",
              "ch.22.48274842R     0.0  0.031796     0.0  ...  0.034908    0.0  0.028587   \n",
              "\n",
              "                 X96.1       X97  X97.1       X98  X98.1       X99  X99.1  \n",
              "ID_REF                                                                     \n",
              "ch.22.909671F      0.0  0.096974    0.0  0.092796    0.0  0.088967    0.0  \n",
              "ch.22.46830341F    0.0  0.034787    0.0  0.078034    0.0  0.053333    0.0  \n",
              "ch.22.1008279F     0.0  0.003545    0.0  0.021802    0.0  0.017240    0.0  \n",
              "ch.22.47579720R    0.0  0.070170    0.0  0.091591    0.0  0.086221    0.0  \n",
              "ch.22.48274842R    0.0  0.031882    0.0  0.032754    0.0  0.033597    0.0  \n",
              "\n",
              "[5 rows x 1464 columns]"
            ]
          },
          "metadata": {},
          "output_type": "display_data"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "fb146f91-1932-47b8-9398-a7bbf5de527e"
      },
      "source": [
        "В таблице для каждого столбца X с данными уровней метилирования сайтов CpG пристуствует дополнительный столбец X.1 со значениями вероятности ошибки в распознавании, разделим эти данные и оставим только те сайты метилирования, для которых p-value не больше 0.01 для не менее чем 95% образцов"
      ],
      "id": "fb146f91-1932-47b8-9398-a7bbf5de527e"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "8528e44c-f745-476a-a332-6c1b5674345c"
      },
      "source": [
        "# Отделим данные метилирования от значений p-value\n",
        "\n",
        "p_value_detection = data_joined[[x for x in data_joined.columns if '.' in x]]\n",
        "\n",
        "data_methylation = data_joined[[x for x in data_joined.columns if '.' not in x]]"
      ],
      "id": "8528e44c-f745-476a-a332-6c1b5674345c",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "a446715d-9204-4a1b-99c0-ee436bd0a1db"
      },
      "source": [
        "p_value_detection.to_csv(path_main_dir+'\\\\preprocessed\\\\p_value_dete')"
      ],
      "id": "a446715d-9204-4a1b-99c0-ee436bd0a1db",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "f02dc2db-43f4-4eaf-9a9d-8b4ced378363"
      },
      "source": [
        "data_methylation.to_csv(path_main_dir+'\\\\preprocessed\\\\data_methylation.csv')"
      ],
      "id": "f02dc2db-43f4-4eaf-9a9d-8b4ced378363",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "50587634",
        "outputId": "77d8d73e-f613-43c7-b8ac-88e9b738c8fd"
      },
      "source": [
        "# оставим только те сайты метилирования, для которых \n",
        "# p-value меньше 0.01 для не менее чем 99% образцов\n",
        "p_value_thresh_sites = p_value_detection.index\\\n",
        "    [((p_value_detection < 0.01).sum(axis = 1)\\\n",
        "      / p_value_detection.shape[1]) >= 0.99]\n",
        "\n",
        "p_value_thresh_sites"
      ],
      "id": "50587634",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/plain": [
              "Index(['cg01707559', 'cg02004872', 'cg02494853', 'cg03244189', 'cg03706273',\n",
              "       'cg04023335', 'cg04462340', 'cg04792227', 'cg04964672', 'cg05213048',\n",
              "       ...\n",
              "       'ch.22.740407F', 'ch.22.757911F', 'ch.22.772318F', 'ch.22.43177094F',\n",
              "       'ch.22.44116734F', 'ch.22.909671F', 'ch.22.46830341F', 'ch.22.1008279F',\n",
              "       'ch.22.47579720R', 'ch.22.48274842R'],\n",
              "      dtype='object', name='ID_REF', length=482878)"
            ]
          },
          "execution_count": 21,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "2d5d89f8-773e-4e23-b29d-be65d9ce6471",
        "outputId": "c209b44f-bd19-499f-bfd5-2a0403385f80"
      },
      "source": [
        "pd.DataFrame(p_value_thresh_sites).to_csv(path_main_dir+'\\\\preprocessed\\\\data_methylation.csv')"
      ],
      "id": "2d5d89f8-773e-4e23-b29d-be65d9ce6471",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>ID_REF</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>cg01707559</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>cg02004872</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>cg02494853</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>cg03244189</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>cg03706273</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>482873</th>\n",
              "      <td>ch.22.909671F</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>482874</th>\n",
              "      <td>ch.22.46830341F</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>482875</th>\n",
              "      <td>ch.22.1008279F</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>482876</th>\n",
              "      <td>ch.22.47579720R</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>482877</th>\n",
              "      <td>ch.22.48274842R</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>482878 rows × 1 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                 ID_REF\n",
              "0            cg01707559\n",
              "1            cg02004872\n",
              "2            cg02494853\n",
              "3            cg03244189\n",
              "4            cg03706273\n",
              "...                 ...\n",
              "482873    ch.22.909671F\n",
              "482874  ch.22.46830341F\n",
              "482875   ch.22.1008279F\n",
              "482876  ch.22.47579720R\n",
              "482877  ch.22.48274842R\n",
              "\n",
              "[482878 rows x 1 columns]"
            ]
          },
          "execution_count": 141,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "49580d63-220f-4ee6-8c25-380ecebb8470"
      },
      "source": [
        "Отбросим столбцы содержащие большинство нолей"
      ],
      "id": "49580d63-220f-4ee6-8c25-380ecebb8470"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "56a0e971-1d98-4547-8422-0001b6f525d8",
        "outputId": "5bd37402-ab33-4099-c28b-12da22e9b76e"
      },
      "source": [
        "fig, axes = plt.subplots(1,1, figsize = (12,5))\n",
        "axes.hist(data_joined.mean(axis=0), bins = 100)\n",
        "plt.title('Распределение среднего значения метилировани образцов')\n",
        "axes.set_ylabel('Количество образцов')\n",
        "axes.set_xlabel('средние β значения уровней метилирования по всем CpG')\n",
        "plt.show()"
      ],
      "id": "56a0e971-1d98-4547-8422-0001b6f525d8",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "image/png": 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\n",
            "text/plain": [
              "<Figure size 864x360 with 1 Axes>"
            ]
          },
          "metadata": {
            "needs_background": "light"
          },
          "output_type": "display_data"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "d3c86a38-6e7a-4a55-8841-ae0ec5d8d13e"
      },
      "source": [
        "del data_1\n",
        "del data_2\n",
        "del data_joined"
      ],
      "id": "d3c86a38-6e7a-4a55-8841-ae0ec5d8d13e",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "bc168a3d-04a8-4509-8d56-01113dc6ba32"
      },
      "source": [
        "## Загрузка описаний образцов"
      ],
      "id": "bc168a3d-04a8-4509-8d56-01113dc6ba32"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "61b9a10f-23a0-4270-bdd0-31d172fa0464"
      },
      "source": [
        "descriptions_samples = pd.read_csv(path_main_dir + '\\\\GSE87571_series_matrix.txt',\n",
        "            sep = '\\t',\n",
        "            header = None,\n",
        "                                   \n",
        "            lineterminator = '!'\n",
        "            ).T"
      ],
      "id": "61b9a10f-23a0-4270-bdd0-31d172fa0464",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "9180b64b-8116-4282-a600-33e2046f9397"
      },
      "source": [
        "for column in descriptions_samples:\n",
        "    descriptions_samples[column] = descriptions_samples[column].str.split('\\n').str[0]"
      ],
      "id": "9180b64b-8116-4282-a600-33e2046f9397",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "48d468d1-7fe0-463c-9376-89515e5b0d01"
      },
      "source": [
        "descriptions_samples.iloc[:, 0] = descriptions_samples.iloc[:, 0].str.split(' genomic DNA from whole blood').str[0]\n",
        "descriptions_samples.columns = descriptions_samples.iloc[0, :]\n",
        "descriptions_samples = descriptions_samples.iloc[1:,:]\n",
        "descriptions_samples = descriptions_samples.set_index('Sample_title', drop = True)\n"
      ],
      "id": "48d468d1-7fe0-463c-9376-89515e5b0d01",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "4861f0f4-dab4-4f84-8b31-7ea12428746e",
        "outputId": "1f6fb317-f5e3-487c-e8fa-bab5479c5323"
      },
      "source": [
        "descriptions_samples.reset_index()"
      ],
      "id": "4861f0f4-dab4-4f84-8b31-7ea12428746e",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Sample_geo_accession</th>\n",
              "      <th>Sample_status</th>\n",
              "      <th>Sample_submission_date</th>\n",
              "      <th>Sample_last_update_date</th>\n",
              "      <th>Sample_type</th>\n",
              "      <th>Sample_channel_count</th>\n",
              "      <th>Sample_source_name_ch1</th>\n",
              "      <th>Sample_organism_ch1</th>\n",
              "      <th>Sample_characteristics_ch1</th>\n",
              "      <th>Sample_characteristics_ch1</th>\n",
              "      <th>...</th>\n",
              "      <th>Sample_contact_address</th>\n",
              "      <th>Sample_contact_city</th>\n",
              "      <th>Sample_contact_state</th>\n",
              "      <th>Sample_contact_zip/postal_code</th>\n",
              "      <th>Sample_contact_country</th>\n",
              "      <th>Sample_supplementary_file</th>\n",
              "      <th>Sample_supplementary_file</th>\n",
              "      <th>Sample_data_row_count</th>\n",
              "      <th>series_matrix_table_begin</th>\n",
              "      <th>series_matrix_table_end</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Sample_title</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>X1</th>\n",
              "      <td>GSM2333901</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 72</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2333901</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X2</th>\n",
              "      <td>GSM2333902</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 55</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2333902</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X3</th>\n",
              "      <td>GSM2333903</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 23</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2333903</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X4</th>\n",
              "      <td>GSM2333904</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 86</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2333904</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X5</th>\n",
              "      <td>GSM2333905</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 74</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2333905</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X728</th>\n",
              "      <td>GSM2334631</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 72</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2334631</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X729</th>\n",
              "      <td>GSM2334632</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 54</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2334632</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X730</th>\n",
              "      <td>GSM2334633</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Female</td>\n",
              "      <td>age: 52</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2334633</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X731</th>\n",
              "      <td>GSM2334634</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Female</td>\n",
              "      <td>age: 45</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2334634</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X732</th>\n",
              "      <td>GSM2334635</td>\n",
              "      <td>Public on Oct 04 2016</td>\n",
              "      <td>Oct 03 2016</td>\n",
              "      <td>Oct 04 2016</td>\n",
              "      <td>genomic</td>\n",
              "      <td>1</td>\n",
              "      <td>whole blood</td>\n",
              "      <td>Homo sapiens</td>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 68</td>\n",
              "      <td>...</td>\n",
              "      <td>BMC, Husarg 3</td>\n",
              "      <td>Uppsala</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>75108</td>\n",
              "      <td>Sweden</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...</td>\n",
              "      <td>0</td>\n",
              "      <td>GSM2334635</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>732 rows × 37 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "0            Sample_geo_accession          Sample_status  \\\n",
              "Sample_title                                               \n",
              "X1                     GSM2333901  Public on Oct 04 2016   \n",
              "X2                     GSM2333902  Public on Oct 04 2016   \n",
              "X3                     GSM2333903  Public on Oct 04 2016   \n",
              "X4                     GSM2333904  Public on Oct 04 2016   \n",
              "X5                     GSM2333905  Public on Oct 04 2016   \n",
              "...                           ...                    ...   \n",
              "X728                   GSM2334631  Public on Oct 04 2016   \n",
              "X729                   GSM2334632  Public on Oct 04 2016   \n",
              "X730                   GSM2334633  Public on Oct 04 2016   \n",
              "X731                   GSM2334634  Public on Oct 04 2016   \n",
              "X732                   GSM2334635  Public on Oct 04 2016   \n",
              "\n",
              "0            Sample_submission_date Sample_last_update_date Sample_type  \\\n",
              "Sample_title                                                              \n",
              "X1                      Oct 03 2016             Oct 04 2016     genomic   \n",
              "X2                      Oct 03 2016             Oct 04 2016     genomic   \n",
              "X3                      Oct 03 2016             Oct 04 2016     genomic   \n",
              "X4                      Oct 03 2016             Oct 04 2016     genomic   \n",
              "X5                      Oct 03 2016             Oct 04 2016     genomic   \n",
              "...                             ...                     ...         ...   \n",
              "X728                    Oct 03 2016             Oct 04 2016     genomic   \n",
              "X729                    Oct 03 2016             Oct 04 2016     genomic   \n",
              "X730                    Oct 03 2016             Oct 04 2016     genomic   \n",
              "X731                    Oct 03 2016             Oct 04 2016     genomic   \n",
              "X732                    Oct 03 2016             Oct 04 2016     genomic   \n",
              "\n",
              "0            Sample_channel_count Sample_source_name_ch1 Sample_organism_ch1  \\\n",
              "Sample_title                                                                   \n",
              "X1                              1            whole blood        Homo sapiens   \n",
              "X2                              1            whole blood        Homo sapiens   \n",
              "X3                              1            whole blood        Homo sapiens   \n",
              "X4                              1            whole blood        Homo sapiens   \n",
              "X5                              1            whole blood        Homo sapiens   \n",
              "...                           ...                    ...                 ...   \n",
              "X728                            1            whole blood        Homo sapiens   \n",
              "X729                            1            whole blood        Homo sapiens   \n",
              "X730                            1            whole blood        Homo sapiens   \n",
              "X731                            1            whole blood        Homo sapiens   \n",
              "X732                            1            whole blood        Homo sapiens   \n",
              "\n",
              "0            Sample_characteristics_ch1 Sample_characteristics_ch1  ...  \\\n",
              "Sample_title                                                        ...   \n",
              "X1                         gender: Male                    age: 72  ...   \n",
              "X2                         gender: Male                    age: 55  ...   \n",
              "X3                         gender: Male                    age: 23  ...   \n",
              "X4                         gender: Male                    age: 86  ...   \n",
              "X5                         gender: Male                    age: 74  ...   \n",
              "...                                 ...                        ...  ...   \n",
              "X728                       gender: Male                    age: 72  ...   \n",
              "X729                       gender: Male                    age: 54  ...   \n",
              "X730                     gender: Female                    age: 52  ...   \n",
              "X731                     gender: Female                    age: 45  ...   \n",
              "X732                       gender: Male                    age: 68  ...   \n",
              "\n",
              "0            Sample_contact_address Sample_contact_city Sample_contact_state  \\\n",
              "Sample_title                                                                   \n",
              "X1                    BMC, Husarg 3             Uppsala               Sweden   \n",
              "X2                    BMC, Husarg 3             Uppsala               Sweden   \n",
              "X3                    BMC, Husarg 3             Uppsala               Sweden   \n",
              "X4                    BMC, Husarg 3             Uppsala               Sweden   \n",
              "X5                    BMC, Husarg 3             Uppsala               Sweden   \n",
              "...                             ...                 ...                  ...   \n",
              "X728                  BMC, Husarg 3             Uppsala               Sweden   \n",
              "X729                  BMC, Husarg 3             Uppsala               Sweden   \n",
              "X730                  BMC, Husarg 3             Uppsala               Sweden   \n",
              "X731                  BMC, Husarg 3             Uppsala               Sweden   \n",
              "X732                  BMC, Husarg 3             Uppsala               Sweden   \n",
              "\n",
              "0            Sample_contact_zip/postal_code Sample_contact_country  \\\n",
              "Sample_title                                                         \n",
              "X1                                    75108                 Sweden   \n",
              "X2                                    75108                 Sweden   \n",
              "X3                                    75108                 Sweden   \n",
              "X4                                    75108                 Sweden   \n",
              "X5                                    75108                 Sweden   \n",
              "...                                     ...                    ...   \n",
              "X728                                  75108                 Sweden   \n",
              "X729                                  75108                 Sweden   \n",
              "X730                                  75108                 Sweden   \n",
              "X731                                  75108                 Sweden   \n",
              "X732                                  75108                 Sweden   \n",
              "\n",
              "0                                     Sample_supplementary_file  \\\n",
              "Sample_title                                                      \n",
              "X1            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "X2            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "X3            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "X4            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "X5            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "...                                                         ...   \n",
              "X728          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "X729          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "X730          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "X731          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "X732          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "\n",
              "0                                     Sample_supplementary_file  \\\n",
              "Sample_title                                                      \n",
              "X1            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "X2            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "X3            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "X4            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "X5            ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2333...   \n",
              "...                                                         ...   \n",
              "X728          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "X729          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "X730          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "X731          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "X732          ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2334...   \n",
              "\n",
              "0            Sample_data_row_count series_matrix_table_begin  \\\n",
              "Sample_title                                                   \n",
              "X1                               0                GSM2333901   \n",
              "X2                               0                GSM2333902   \n",
              "X3                               0                GSM2333903   \n",
              "X4                               0                GSM2333904   \n",
              "X5                               0                GSM2333905   \n",
              "...                            ...                       ...   \n",
              "X728                             0                GSM2334631   \n",
              "X729                             0                GSM2334632   \n",
              "X730                             0                GSM2334633   \n",
              "X731                             0                GSM2334634   \n",
              "X732                             0                GSM2334635   \n",
              "\n",
              "0            series_matrix_table_end  \n",
              "Sample_title                          \n",
              "X1                               NaN  \n",
              "X2                               NaN  \n",
              "X3                               NaN  \n",
              "X4                               NaN  \n",
              "X5                               NaN  \n",
              "...                              ...  \n",
              "X728                             NaN  \n",
              "X729                             NaN  \n",
              "X730                             NaN  \n",
              "X731                             NaN  \n",
              "X732                             NaN  \n",
              "\n",
              "[732 rows x 37 columns]"
            ]
          },
          "execution_count": 98,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "4032a101-aa09-4e29-83bb-98360542a47f",
        "outputId": "b6f7b0bb-fea7-41b0-d02d-82d401570fc3"
      },
      "source": [
        "descriptions_samples['Sample_characteristics_ch1']"
      ],
      "id": "4032a101-aa09-4e29-83bb-98360542a47f",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/html": [
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Sample_characteristics_ch1</th>\n",
              "      <th>Sample_characteristics_ch1</th>\n",
              "      <th>Sample_characteristics_ch1</th>\n",
              "      <th>Sample_characteristics_ch1</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Sample_title</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>X1</th>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 72</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X2</th>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 55</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X3</th>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 23</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X4</th>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 86</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X5</th>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 74</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X728</th>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 72</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X729</th>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 54</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X730</th>\n",
              "      <td>gender: Female</td>\n",
              "      <td>age: 52</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X731</th>\n",
              "      <td>gender: Female</td>\n",
              "      <td>age: 45</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X732</th>\n",
              "      <td>gender: Male</td>\n",
              "      <td>age: 68</td>\n",
              "      <td>tissue: whole blood</td>\n",
              "      <td>disease state: normal</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>732 rows × 4 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "0            Sample_characteristics_ch1 Sample_characteristics_ch1  \\\n",
              "Sample_title                                                         \n",
              "X1                         gender: Male                    age: 72   \n",
              "X2                         gender: Male                    age: 55   \n",
              "X3                         gender: Male                    age: 23   \n",
              "X4                         gender: Male                    age: 86   \n",
              "X5                         gender: Male                    age: 74   \n",
              "...                                 ...                        ...   \n",
              "X728                       gender: Male                    age: 72   \n",
              "X729                       gender: Male                    age: 54   \n",
              "X730                     gender: Female                    age: 52   \n",
              "X731                     gender: Female                    age: 45   \n",
              "X732                       gender: Male                    age: 68   \n",
              "\n",
              "0            Sample_characteristics_ch1 Sample_characteristics_ch1  \n",
              "Sample_title                                                        \n",
              "X1                  tissue: whole blood      disease state: normal  \n",
              "X2                  tissue: whole blood      disease state: normal  \n",
              "X3                  tissue: whole blood      disease state: normal  \n",
              "X4                  tissue: whole blood      disease state: normal  \n",
              "X5                  tissue: whole blood      disease state: normal  \n",
              "...                                 ...                        ...  \n",
              "X728                tissue: whole blood      disease state: normal  \n",
              "X729                tissue: whole blood      disease state: normal  \n",
              "X730                tissue: whole blood      disease state: normal  \n",
              "X731                tissue: whole blood      disease state: normal  \n",
              "X732                tissue: whole blood      disease state: normal  \n",
              "\n",
              "[732 rows x 4 columns]"
            ]
          },
          "execution_count": 109,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "0e205f4a-e566-4387-a2e4-fc8381d3eecc"
      },
      "source": [
        "gender_age_tissue_state = descriptions_samples.iloc[:, [ 8,  9, 10, 11]]\n",
        "gender_age_tissue_state.columns = ['sex', 'age', 'tissue', 'disease_state']"
      ],
      "id": "0e205f4a-e566-4387-a2e4-fc8381d3eecc",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "c34bbae3-42bf-42be-9731-8441399ae979"
      },
      "source": [
        "descriptions_samples = descriptions_samples[['Sample_geo_accession']].join(gender_age_tissue_state, how = 'outer')"
      ],
      "id": "c34bbae3-42bf-42be-9731-8441399ae979",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "6ccf514b-8286-4280-a461-0360303b6ffc"
      },
      "source": [
        "descriptions_samples.sex = descriptions_samples.sex.str.split('gender: ').str[1]\n",
        "descriptions_samples.age = descriptions_samples.age.str.split('age: ').str[1]\n",
        "descriptions_samples = descriptions_samples.drop(['tissue', 'disease_state'], axis = 1)"
      ],
      "id": "6ccf514b-8286-4280-a461-0360303b6ffc",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "0d8b6bf9-5b54-45b2-91a1-c6c688c1a72f"
      },
      "source": [
        " descriptions_samples = descriptions_samples.dropna(axis = 0, how = 'any')"
      ],
      "id": "0d8b6bf9-5b54-45b2-91a1-c6c688c1a72f",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "787d3a14-0d8e-4fa2-a381-34f0607859e3"
      },
      "source": [
        "descriptions_samples = descriptions_samples[descriptions_samples.age != 'NA']\n",
        "\n",
        "descriptions_samples.age = descriptions_samples.age.astype('int32')"
      ],
      "id": "787d3a14-0d8e-4fa2-a381-34f0607859e3",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "d2563def-a82b-4fa3-9ddf-0c7a8f4982fd"
      },
      "source": [
        "descriptions.to_csv(path_main_dir+'\\\\GSE87571_preprocessed\\\\sample_descriptions.cvs')"
      ],
      "id": "d2563def-a82b-4fa3-9ddf-0c7a8f4982fd",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "c79e26a9-c9ae-44df-9135-d5594e6f926a"
      },
      "source": [
        "descriptions = pd.read_csv(path_main_dir\\\n",
        "                           + r\"\\GSE87571_preprocessed\"\n",
        "                           + r\"\\descriptions_samples.csv\",\n",
        "                           index_col = 0\n",
        "                          )"
      ],
      "id": "c79e26a9-c9ae-44df-9135-d5594e6f926a",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "e58e5325-9106-4f78-90bd-e6338852676f",
        "outputId": "1094f3ee-f223-4079-e3c8-381724a62d0a"
      },
      "source": [
        "descriptions"
      ],
      "id": "e58e5325-9106-4f78-90bd-e6338852676f",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Sample_geo_accession</th>\n",
              "      <th>sex</th>\n",
              "      <th>age</th>\n",
              "      <th>group</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>X1</th>\n",
              "      <td>GSM2333901</td>\n",
              "      <td>Male</td>\n",
              "      <td>72</td>\n",
              "      <td>70_74</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X2</th>\n",
              "      <td>GSM2333902</td>\n",
              "      <td>Male</td>\n",
              "      <td>55</td>\n",
              "      <td>55_59</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X3</th>\n",
              "      <td>GSM2333903</td>\n",
              "      <td>Male</td>\n",
              "      <td>23</td>\n",
              "      <td>20_24</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X4</th>\n",
              "      <td>GSM2333904</td>\n",
              "      <td>Male</td>\n",
              "      <td>86</td>\n",
              "      <td>85_89</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X5</th>\n",
              "      <td>GSM2333905</td>\n",
              "      <td>Male</td>\n",
              "      <td>74</td>\n",
              "      <td>70_74</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X728</th>\n",
              "      <td>GSM2334631</td>\n",
              "      <td>Male</td>\n",
              "      <td>72</td>\n",
              "      <td>70_74</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X729</th>\n",
              "      <td>GSM2334632</td>\n",
              "      <td>Male</td>\n",
              "      <td>54</td>\n",
              "      <td>50_54</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X730</th>\n",
              "      <td>GSM2334633</td>\n",
              "      <td>Female</td>\n",
              "      <td>52</td>\n",
              "      <td>50_54</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X731</th>\n",
              "      <td>GSM2334634</td>\n",
              "      <td>Female</td>\n",
              "      <td>45</td>\n",
              "      <td>45_49</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X732</th>\n",
              "      <td>GSM2334635</td>\n",
              "      <td>Male</td>\n",
              "      <td>68</td>\n",
              "      <td>65_69</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>729 rows × 4 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     Sample_geo_accession     sex  age  group\n",
              "X1             GSM2333901    Male   72  70_74\n",
              "X2             GSM2333902    Male   55  55_59\n",
              "X3             GSM2333903    Male   23  20_24\n",
              "X4             GSM2333904    Male   86  85_89\n",
              "X5             GSM2333905    Male   74  70_74\n",
              "...                   ...     ...  ...    ...\n",
              "X728           GSM2334631    Male   72  70_74\n",
              "X729           GSM2334632    Male   54  50_54\n",
              "X730           GSM2334633  Female   52  50_54\n",
              "X731           GSM2334634  Female   45  45_49\n",
              "X732           GSM2334635    Male   68  65_69\n",
              "\n",
              "[729 rows x 4 columns]"
            ]
          },
          "execution_count": 126,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "da1a0d76-3953-424d-97aa-4255a628024b",
        "outputId": "be3f8e61-aba4-418a-d093-c4bc264e4553"
      },
      "source": [
        "fig, axes = plt.subplots(1,1, figsize = (12,5))\n",
        "\n",
        "axes.hist(descriptions[descriptions['sex'] == 'Male']['age'].sort_values(),\n",
        "         bins = 50,\n",
        "         alpha=0.7,\n",
        "         label = 'Male'\n",
        "        )\n",
        "axes.hist(descriptions[descriptions['sex'] == 'Female']['age'].sort_values(),\n",
        "         bins = 50,\n",
        "         alpha=0.7,\n",
        "         label = 'Female'\n",
        "        )\n",
        "plt.title('Распределение образцов по возрасту и полу')\n",
        "axes.set_ylabel('Количество образцов')\n",
        "axes.set_xlabel('Возраст (лет)')\n",
        "plt.legend()\n",
        "plt.show()"
      ],
      "id": "da1a0d76-3953-424d-97aa-4255a628024b",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "image/png": 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\n",
            "text/plain": [
              "<Figure size 864x360 with 1 Axes>"
            ]
          },
          "metadata": {
            "needs_background": "light"
          },
          "output_type": "display_data"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "b68bfa53-a253-4a5c-930c-c681de020385"
      },
      "source": [
        "## Предобработка дополнительных описаний образцов"
      ],
      "id": "b68bfa53-a253-4a5c-930c-c681de020385"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "76cb7f66-2257-452d-817d-d0a513b6cbd0",
        "outputId": "44d3165b-09d3-4989-abcb-47285377fc9a"
      },
      "source": [
        "additional_desriptions = pd.read_excel(path_main_dir+'\\\\GSE87571_additional_sample_chararcteristics.xlsx',\n",
        "                                      )"
      ],
      "id": "76cb7f66-2257-452d-817d-d0a513b6cbd0",
      "execution_count": null,
      "outputs": [
        {
          "name": "stderr",
          "output_type": "stream",
          "text": [
            "C:\\Users\\IvanovNikita\\miniconda3\\lib\\site-packages\\openpyxl\\worksheet\\_reader.py:312: UserWarning: Unknown extension is not supported and will be removed\n",
            "  warn(msg)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "77efe8e7-90c5-4eed-94ad-269df5af926c"
      },
      "source": [
        "additional_desriptions.columns = additional_desriptions.columns.str.split('characteristics:').str[1]"
      ],
      "id": "77efe8e7-90c5-4eed-94ad-269df5af926c",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "d807884b-a0bb-4558-8b72-e0d7701fce18"
      },
      "source": [
        "additional_desriptions = additional_desriptions.join(descriptions[['Sample_geo_accession']], how = 'left')"
      ],
      "id": "d807884b-a0bb-4558-8b72-e0d7701fce18",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "ac987d91-ce49-47c8-a8ca-a60804a1463a"
      },
      "source": [
        "additional_desriptions['Sample_geo_accession'] = additional_desriptions.iloc[:, 0]"
      ],
      "id": "ac987d91-ce49-47c8-a8ca-a60804a1463a",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "d50f7486-53fb-4a4b-a4f7-0f02050ebf81"
      },
      "source": [
        "additional_desriptions  = additional_desriptions.set_index('Sample_geo_accession', drop = True)"
      ],
      "id": "d50f7486-53fb-4a4b-a4f7-0f02050ebf81",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "98789197-279c-4aaa-8324-6821d44523bd"
      },
      "source": [
        "additional_desriptions = additional_desriptions\\\n",
        "    .join(descriptions[['Sample_geo_accession']].reset_index().set_index('Sample_geo_accession'))"
      ],
      "id": "98789197-279c-4aaa-8324-6821d44523bd",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "7c860c18-7dd0-4d0f-b0be-87f9501ca7a8",
        "outputId": "8f3389b4-092c-4d6d-f58a-f322988ff782"
      },
      "source": [
        "additional_desriptions = additional_desriptions.set_index('index', drop = True)\n",
        "additional_desriptions"
      ],
      "id": "7c860c18-7dd0-4d0f-b0be-87f9501ca7a8",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>NaN</th>\n",
              "      <th>year_of_collection</th>\n",
              "      <th>smoke</th>\n",
              "      <th>rs28403969:1999006:G:A</th>\n",
              "      <th>rs142891527:2180528:G:A</th>\n",
              "      <th>rs75126985:6425349:C:T</th>\n",
              "      <th>rs1497856:74289939:C:G</th>\n",
              "      <th>rs12741890:81645181:C:T</th>\n",
              "      <th>rs76624861:85416840:C:T</th>\n",
              "      <th>rs12133641:154428283:A:G</th>\n",
              "      <th>...</th>\n",
              "      <th>Sample_Group</th>\n",
              "      <th>CD8T</th>\n",
              "      <th>CD4T</th>\n",
              "      <th>NK</th>\n",
              "      <th>Bcell</th>\n",
              "      <th>Mono</th>\n",
              "      <th>Gran</th>\n",
              "      <th>KA</th>\n",
              "      <th>Slide</th>\n",
              "      <th>chip:ass</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>index</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>X1</th>\n",
              "      <td>GSM2333901</td>\n",
              "      <td>2006</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.007</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>1.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2013</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.100050</td>\n",
              "      <td>0.103269</td>\n",
              "      <td>0.015374</td>\n",
              "      <td>0.051578</td>\n",
              "      <td>0.728901</td>\n",
              "      <td>KA06</td>\n",
              "      <td>9370847096</td>\n",
              "      <td>7.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X2</th>\n",
              "      <td>GSM2333902</td>\n",
              "      <td>2006</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.007</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>2.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2013</td>\n",
              "      <td>0.007585</td>\n",
              "      <td>0.219594</td>\n",
              "      <td>0.097459</td>\n",
              "      <td>0.036715</td>\n",
              "      <td>0.094437</td>\n",
              "      <td>0.553426</td>\n",
              "      <td>KA06</td>\n",
              "      <td>9376538120</td>\n",
              "      <td>7.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X3</th>\n",
              "      <td>GSM2333903</td>\n",
              "      <td>2006</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.660</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>1.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2012</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.018278</td>\n",
              "      <td>0.005066</td>\n",
              "      <td>0.035204</td>\n",
              "      <td>0.092227</td>\n",
              "      <td>0.827294</td>\n",
              "      <td>KA06</td>\n",
              "      <td>7766148053</td>\n",
              "      <td>7.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X4</th>\n",
              "      <td>GSM2333904</td>\n",
              "      <td>2006</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.387</td>\n",
              "      <td>0.000</td>\n",
              "      <td>1.0</td>\n",
              "      <td>1.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.059</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2012</td>\n",
              "      <td>0.024722</td>\n",
              "      <td>0.179235</td>\n",
              "      <td>0.152868</td>\n",
              "      <td>0.020081</td>\n",
              "      <td>0.113306</td>\n",
              "      <td>0.496979</td>\n",
              "      <td>KA06</td>\n",
              "      <td>7766148077</td>\n",
              "      <td>7.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X5</th>\n",
              "      <td>GSM2333905</td>\n",
              "      <td>2006</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.003</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>1.000</td>\n",
              "      <td>1.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2013</td>\n",
              "      <td>0.012076</td>\n",
              "      <td>0.208174</td>\n",
              "      <td>0.068129</td>\n",
              "      <td>0.047263</td>\n",
              "      <td>0.087617</td>\n",
              "      <td>0.581739</td>\n",
              "      <td>KA06</td>\n",
              "      <td>9370847096</td>\n",
              "      <td>7.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X728</th>\n",
              "      <td>GSM2334631</td>\n",
              "      <td>2009</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>1.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2012</td>\n",
              "      <td>0.112239</td>\n",
              "      <td>0.238704</td>\n",
              "      <td>0.086998</td>\n",
              "      <td>0.087370</td>\n",
              "      <td>0.072453</td>\n",
              "      <td>0.430909</td>\n",
              "      <td>KA09</td>\n",
              "      <td>7766148080</td>\n",
              "      <td>3.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X729</th>\n",
              "      <td>GSM2334632</td>\n",
              "      <td>2009</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>1.0</td>\n",
              "      <td>0.121</td>\n",
              "      <td>0.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2012</td>\n",
              "      <td>0.130784</td>\n",
              "      <td>0.234445</td>\n",
              "      <td>0.091153</td>\n",
              "      <td>0.076919</td>\n",
              "      <td>0.067728</td>\n",
              "      <td>0.426284</td>\n",
              "      <td>KA09</td>\n",
              "      <td>7766148080</td>\n",
              "      <td>3.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X730</th>\n",
              "      <td>GSM2334633</td>\n",
              "      <td>2009</td>\n",
              "      <td>2.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.005</td>\n",
              "      <td>0.0</td>\n",
              "      <td>2.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.004</td>\n",
              "      <td>0.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2012</td>\n",
              "      <td>0.122360</td>\n",
              "      <td>0.154988</td>\n",
              "      <td>0.032996</td>\n",
              "      <td>0.065739</td>\n",
              "      <td>0.101473</td>\n",
              "      <td>0.547858</td>\n",
              "      <td>KA09</td>\n",
              "      <td>7766148084</td>\n",
              "      <td>4.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X731</th>\n",
              "      <td>GSM2334634</td>\n",
              "      <td>2009</td>\n",
              "      <td>0.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.000</td>\n",
              "      <td>0.0</td>\n",
              "      <td>1.008</td>\n",
              "      <td>1.0</td>\n",
              "      <td>0.000</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2012</td>\n",
              "      <td>0.114023</td>\n",
              "      <td>0.114189</td>\n",
              "      <td>0.013537</td>\n",
              "      <td>0.055544</td>\n",
              "      <td>0.103036</td>\n",
              "      <td>0.628838</td>\n",
              "      <td>KA09</td>\n",
              "      <td>7766148080</td>\n",
              "      <td>3.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>X732</th>\n",
              "      <td>GSM2334635</td>\n",
              "      <td>2009</td>\n",
              "      <td>2.0</td>\n",
              "      <td>1.000</td>\n",
              "      <td>0.890</td>\n",
              "      <td>0.0</td>\n",
              "      <td>2.000</td>\n",
              "      <td>1.0</td>\n",
              "      <td>0.562</td>\n",
              "      <td>1.0</td>\n",
              "      <td>...</td>\n",
              "      <td>2012</td>\n",
              "      <td>0.176210</td>\n",
              "      <td>0.134686</td>\n",
              "      <td>0.173033</td>\n",
              "      <td>0.039963</td>\n",
              "      <td>0.140599</td>\n",
              "      <td>0.341829</td>\n",
              "      <td>KA09</td>\n",
              "      <td>7766148053</td>\n",
              "      <td>3.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>732 rows × 181 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "              NaN   year_of_collection   smoke   rs28403969:1999006:G:A  \\\n",
              "index                                                                     \n",
              "X1     GSM2333901                 2006     0.0                    0.007   \n",
              "X2     GSM2333902                 2006     0.0                    0.007   \n",
              "X3     GSM2333903                 2006     0.0                    0.660   \n",
              "X4     GSM2333904                 2006     0.0                    0.387   \n",
              "X5     GSM2333905                 2006     0.0                    0.003   \n",
              "...           ...                  ...     ...                      ...   \n",
              "X728   GSM2334631                 2009     0.0                    0.000   \n",
              "X729   GSM2334632                 2009     0.0                    0.000   \n",
              "X730   GSM2334633                 2009     2.0                    0.000   \n",
              "X731   GSM2334634                 2009     0.0                    0.000   \n",
              "X732   GSM2334635                 2009     2.0                    1.000   \n",
              "\n",
              "        rs142891527:2180528:G:A   rs75126985:6425349:C:T  \\\n",
              "index                                                      \n",
              "X1                        0.000                      0.0   \n",
              "X2                        0.000                      0.0   \n",
              "X3                        0.000                      0.0   \n",
              "X4                        0.000                      1.0   \n",
              "X5                        0.000                      0.0   \n",
              "...                         ...                      ...   \n",
              "X728                      0.000                      0.0   \n",
              "X729                      0.000                      0.0   \n",
              "X730                      0.005                      0.0   \n",
              "X731                      0.000                      0.0   \n",
              "X732                      0.890                      0.0   \n",
              "\n",
              "        rs1497856:74289939:C:G   rs12741890:81645181:C:T  \\\n",
              "index                                                      \n",
              "X1                       1.000                       0.0   \n",
              "X2                       2.000                       0.0   \n",
              "X3                       1.000                       0.0   \n",
              "X4                       1.000                       0.0   \n",
              "X5                       1.000                       1.0   \n",
              "...                        ...                       ...   \n",
              "X728                     1.000                       0.0   \n",
              "X729                     0.000                       1.0   \n",
              "X730                     2.000                       0.0   \n",
              "X731                     1.008                       1.0   \n",
              "X732                     2.000                       1.0   \n",
              "\n",
              "        rs76624861:85416840:C:T   rs12133641:154428283:A:G  ...  \\\n",
              "index                                                       ...   \n",
              "X1                        0.000                        1.0  ...   \n",
              "X2                        0.000                        0.0  ...   \n",
              "X3                        0.000                        0.0  ...   \n",
              "X4                        0.059                        1.0  ...   \n",
              "X5                        0.000                        0.0  ...   \n",
              "...                         ...                        ...  ...   \n",
              "X728                      0.000                        0.0  ...   \n",
              "X729                      0.121                        0.0  ...   \n",
              "X730                      0.004                        0.0  ...   \n",
              "X731                      0.000                        1.0  ...   \n",
              "X732                      0.562                        1.0  ...   \n",
              "\n",
              "        Sample_Group      CD8T      CD4T        NK     Bcell      Mono  \\\n",
              "index                                                                    \n",
              "X1              2013  0.000000  0.100050  0.103269  0.015374  0.051578   \n",
              "X2              2013  0.007585  0.219594  0.097459  0.036715  0.094437   \n",
              "X3              2012  0.000000  0.018278  0.005066  0.035204  0.092227   \n",
              "X4              2012  0.024722  0.179235  0.152868  0.020081  0.113306   \n",
              "X5              2013  0.012076  0.208174  0.068129  0.047263  0.087617   \n",
              "...              ...       ...       ...       ...       ...       ...   \n",
              "X728            2012  0.112239  0.238704  0.086998  0.087370  0.072453   \n",
              "X729            2012  0.130784  0.234445  0.091153  0.076919  0.067728   \n",
              "X730            2012  0.122360  0.154988  0.032996  0.065739  0.101473   \n",
              "X731            2012  0.114023  0.114189  0.013537  0.055544  0.103036   \n",
              "X732            2012  0.176210  0.134686  0.173033  0.039963  0.140599   \n",
              "\n",
              "           Gran    KA       Slide   chip:ass  \n",
              "index                                         \n",
              "X1     0.728901  KA06  9370847096        7.0  \n",
              "X2     0.553426  KA06  9376538120        7.0  \n",
              "X3     0.827294  KA06  7766148053        7.0  \n",
              "X4     0.496979  KA06  7766148077        7.0  \n",
              "X5     0.581739  KA06  9370847096        7.0  \n",
              "...         ...   ...         ...        ...  \n",
              "X728   0.430909  KA09  7766148080        3.0  \n",
              "X729   0.426284  KA09  7766148080        3.0  \n",
              "X730   0.547858  KA09  7766148084        4.0  \n",
              "X731   0.628838  KA09  7766148080        3.0  \n",
              "X732   0.341829  KA09  7766148053        3.0  \n",
              "\n",
              "[732 rows x 181 columns]"
            ]
          },
          "execution_count": 22,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "9eb8bf07-0728-42f4-978d-d2e84caf707e"
      },
      "source": [
        "additional_desriptions.to_csv(path_main_dir+\"\\\\GSE87571_preprocessed\\\\additional_desriptions.csv\")"
      ],
      "id": "9eb8bf07-0728-42f4-978d-d2e84caf707e",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "279ddf59-cebf-4cbd-8ca0-826df023a5ed"
      },
      "source": [
        "## Загрузка описаний сайтов метилирования"
      ],
      "id": "279ddf59-cebf-4cbd-8ca0-826df023a5ed"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "8e5acf2d-e7a6-4d6b-a398-0e86523ada8e",
        "outputId": "6287eced-50be-4bbd-c193-46f13ebdad80"
      },
      "source": [
        "sites_descriptions = pd.read_csv(path_main_dir+'\\\\GPL13534-tbl-1.txt', sep = '\t')"
      ],
      "id": "8e5acf2d-e7a6-4d6b-a398-0e86523ada8e",
      "execution_count": null,
      "outputs": [
        {
          "name": "stderr",
          "output_type": "stream",
          "text": [
            "C:\\Users\\IvanovNikita\\miniconda3\\lib\\site-packages\\IPython\\core\\interactiveshell.py:3169: DtypeWarning: Columns (11,14,15,36) have mixed types.Specify dtype option on import or set low_memory=False.\n",
            "  has_raised = await self.run_ast_nodes(code_ast.body, cell_name,\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "26b82edc-b0b1-4d64-bb59-03f1150750b9",
        "outputId": "81c5a3b3-ca02-4695-ea19-c01a951c6b46"
      },
      "source": [
        "sites_descriptions.columns = ['ID',\n",
        "                              'Name',\n",
        "                              'AddressA_ID',\n",
        "                              'AlleleA_ProbeSeq',\n",
        "                              'AddressB_ID',\n",
        "                              'AlleleB_ProbeSeq',\n",
        "                              'Infinium_Design_Type',\n",
        "                              'Next_Base',\n",
        "                              'Color_Channel',\n",
        "                              'Forward_Sequence',\n",
        "                              'Genome_Build',\n",
        "                              'CHR',\n",
        "                              'MAPINFO',\n",
        "                              'SourceSeq',\n",
        "                              'Chromosome_36',\n",
        "                              'Coordinate_36',\n",
        "                              'Strand',\n",
        "                              'Probe_SNPs',\n",
        "                              'Probe_SNPs_10',\n",
        "                              'Random_Loci',\n",
        "                              'Methyl27_Loci',\n",
        "                              'UCSC_RefGene_Name',\n",
        "                              'UCSC_RefGene_Accession',\n",
        "                              'UCSC_RefGene_Group',\n",
        "                              'UCSC_CpG_Islands_Name',\n",
        "                              'Relation_to_UCSC_CpG_Island',\n",
        "                              'Phantom',\n",
        "                              'DMR',\n",
        "                              'Enhancer',\n",
        "                              'HMM_Island',\n",
        "                              'Regulatory_Feature_Name',\n",
        "                              'Regulatory_Feature_Group',\n",
        "                              'DHS',\n",
        "                              'RANGE_START',\n",
        "                              'RANGE_END',\n",
        "                              'RANGE_GB',\n",
        "                              'SPOT_ID']\n",
        "sites_descriptions"
      ],
      "id": "26b82edc-b0b1-4d64-bb59-03f1150750b9",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/html": [
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              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>ID</th>\n",
              "      <th>Name</th>\n",
              "      <th>AddressA_ID</th>\n",
              "      <th>AlleleA_ProbeSeq</th>\n",
              "      <th>AddressB_ID</th>\n",
              "      <th>AlleleB_ProbeSeq</th>\n",
              "      <th>Infinium_Design_Type</th>\n",
              "      <th>Next_Base</th>\n",
              "      <th>Color_Channel</th>\n",
              "      <th>Forward_Sequence</th>\n",
              "      <th>...</th>\n",
              "      <th>DMR</th>\n",
              "      <th>Enhancer</th>\n",
              "      <th>HMM_Island</th>\n",
              "      <th>Regulatory_Feature_Name</th>\n",
              "      <th>Regulatory_Feature_Group</th>\n",
              "      <th>DHS</th>\n",
              "      <th>RANGE_START</th>\n",
              "      <th>RANGE_END</th>\n",
              "      <th>RANGE_GB</th>\n",
              "      <th>SPOT_ID</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
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              "      <th>0</th>\n",
              "      <td>cg00050873</td>\n",
              "      <td>cg00050873</td>\n",
              "      <td>32735311</td>\n",
              "      <td>ACAAAAAAACAACACACAACTATAATAATTTTTAAAATAAATAAAC...</td>\n",
              "      <td>31717405.0</td>\n",
              "      <td>ACGAAAAAACAACGCACAACTATAATAATTTTTAAAATAAATAAAC...</td>\n",
              "      <td>I</td>\n",
              "      <td>A</td>\n",
              "      <td>Red</td>\n",
              "      <td>TATCTCTGTCTGGCGAGGAGGCAACGCACAACTGTGGTGGTTTTTG...</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>Y:9973136-9976273</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>9363356.0</td>\n",
              "      <td>9363479.0</td>\n",
              "      <td>NC_000024.9</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>cg00061679</td>\n",
              "      <td>cg00061679</td>\n",
              "      <td>28780415</td>\n",
              "      <td>AAAACATTAAAAAACTAATTCACTACTATTTAATTACTTTATTTTC...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>TCAACAAATGAGAGACATTGAAGAACTAATTCACTACTATTTGGTT...</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>25314171.0</td>\n",
              "      <td>25314294.0</td>\n",
              "      <td>NC_000024.9</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>cg00063477</td>\n",
              "      <td>cg00063477</td>\n",
              "      <td>16712347</td>\n",
              "      <td>TATTCTTCCACACAAAATACTAAACRTATATTTACAAAAATACTTC...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>CTCCTGTACTTGTTCATTAAATAATGATTCCTTGGATATACCAAGT...</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>22741795.0</td>\n",
              "      <td>22741918.0</td>\n",
              "      <td>NC_000024.9</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>cg00121626</td>\n",
              "      <td>cg00121626</td>\n",
              "      <td>19779393</td>\n",
              "      <td>AAAACTAATAAAAATAACTTACAAACCAAATACTATACCCTACAAC...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>AGGTGAATGAAGAGACTAATGGGAGTGGCTTGCAAGCCAGGTACTG...</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>21664296.0</td>\n",
              "      <td>21664419.0</td>\n",
              "      <td>NC_000024.9</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>cg00212031</td>\n",
              "      <td>cg00212031</td>\n",
              "      <td>29674443</td>\n",
              "      <td>CCCAATTAACCACAAAAACTAAACAAATTATACAATCAAAAAAACA...</td>\n",
              "      <td>38703326.0</td>\n",
              "      <td>CCCAATTAACCGCAAAAACTAAACAAATTATACGATCGAAAAAACG...</td>\n",
              "      <td>I</td>\n",
              "      <td>T</td>\n",
              "      <td>Red</td>\n",
              "      <td>CCATTGGCCCGCCCCAGTTGGCCGCAGGGACTGAGCAAGTTATGCG...</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>Y:19697854-19699393</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>21239348.0</td>\n",
              "      <td>21239471.0</td>\n",
              "      <td>NC_000024.9</td>\n",
              "      <td>NaN</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>485571</th>\n",
              "      <td>rs7746156</td>\n",
              "      <td>rs7746156</td>\n",
              "      <td>33622366</td>\n",
              "      <td>TACCAACCAATACTCAAAATAACCCATACTAATCTTCCTATTCTTC...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>rs7746156</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>485572</th>\n",
              "      <td>rs1945975</td>\n",
              "      <td>rs1945975</td>\n",
              "      <td>23614475</td>\n",
              "      <td>CCACTTCTCTTTCCTCACCTACTTTCATTTAATTTAATACTTACCT...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>rs1945975</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>485573</th>\n",
              "      <td>rs966367</td>\n",
              "      <td>rs966367</td>\n",
              "      <td>16795360</td>\n",
              "      <td>ATAACTCCTTTAACTTTAAACACACATCTCTACACACAACCACATA...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>rs966367</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>485574</th>\n",
              "      <td>rs877309</td>\n",
              "      <td>rs877309</td>\n",
              "      <td>54760445</td>\n",
              "      <td>CCCCAACCCAAAACCTCTATAATTCACAAAACACAAATTCACACTT...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>rs877309</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>485575</th>\n",
              "      <td>rs4331560</td>\n",
              "      <td>rs4331560</td>\n",
              "      <td>10654345</td>\n",
              "      <td>CATAACATTTCTCATCCAATAACTCACTCCATCTTCCAATACTCCC...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>rs4331560</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>485576 rows × 37 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                ID        Name  AddressA_ID  \\\n",
              "0       cg00050873  cg00050873     32735311   \n",
              "1       cg00061679  cg00061679     28780415   \n",
              "2       cg00063477  cg00063477     16712347   \n",
              "3       cg00121626  cg00121626     19779393   \n",
              "4       cg00212031  cg00212031     29674443   \n",
              "...            ...         ...          ...   \n",
              "485571   rs7746156   rs7746156     33622366   \n",
              "485572   rs1945975   rs1945975     23614475   \n",
              "485573    rs966367    rs966367     16795360   \n",
              "485574    rs877309    rs877309     54760445   \n",
              "485575   rs4331560   rs4331560     10654345   \n",
              "\n",
              "                                         AlleleA_ProbeSeq  AddressB_ID  \\\n",
              "0       ACAAAAAAACAACACACAACTATAATAATTTTTAAAATAAATAAAC...   31717405.0   \n",
              "1       AAAACATTAAAAAACTAATTCACTACTATTTAATTACTTTATTTTC...          NaN   \n",
              "2       TATTCTTCCACACAAAATACTAAACRTATATTTACAAAAATACTTC...          NaN   \n",
              "3       AAAACTAATAAAAATAACTTACAAACCAAATACTATACCCTACAAC...          NaN   \n",
              "4       CCCAATTAACCACAAAAACTAAACAAATTATACAATCAAAAAAACA...   38703326.0   \n",
              "...                                                   ...          ...   \n",
              "485571  TACCAACCAATACTCAAAATAACCCATACTAATCTTCCTATTCTTC...          NaN   \n",
              "485572  CCACTTCTCTTTCCTCACCTACTTTCATTTAATTTAATACTTACCT...          NaN   \n",
              "485573  ATAACTCCTTTAACTTTAAACACACATCTCTACACACAACCACATA...          NaN   \n",
              "485574  CCCCAACCCAAAACCTCTATAATTCACAAAACACAAATTCACACTT...          NaN   \n",
              "485575  CATAACATTTCTCATCCAATAACTCACTCCATCTTCCAATACTCCC...          NaN   \n",
              "\n",
              "                                         AlleleB_ProbeSeq  \\\n",
              "0       ACGAAAAAACAACGCACAACTATAATAATTTTTAAAATAAATAAAC...   \n",
              "1                                                     NaN   \n",
              "2                                                     NaN   \n",
              "3                                                     NaN   \n",
              "4       CCCAATTAACCGCAAAAACTAAACAAATTATACGATCGAAAAAACG...   \n",
              "...                                                   ...   \n",
              "485571                                                NaN   \n",
              "485572                                                NaN   \n",
              "485573                                                NaN   \n",
              "485574                                                NaN   \n",
              "485575                                                NaN   \n",
              "\n",
              "       Infinium_Design_Type Next_Base Color_Channel  \\\n",
              "0                         I         A           Red   \n",
              "1                        II       NaN           NaN   \n",
              "2                        II       NaN           NaN   \n",
              "3                        II       NaN           NaN   \n",
              "4                         I         T           Red   \n",
              "...                     ...       ...           ...   \n",
              "485571                   II       NaN           NaN   \n",
              "485572                   II       NaN           NaN   \n",
              "485573                   II       NaN           NaN   \n",
              "485574                   II       NaN           NaN   \n",
              "485575                   II       NaN           NaN   \n",
              "\n",
              "                                         Forward_Sequence  ...  DMR Enhancer  \\\n",
              "0       TATCTCTGTCTGGCGAGGAGGCAACGCACAACTGTGGTGGTTTTTG...  ...  NaN      NaN   \n",
              "1       TCAACAAATGAGAGACATTGAAGAACTAATTCACTACTATTTGGTT...  ...  NaN      NaN   \n",
              "2       CTCCTGTACTTGTTCATTAAATAATGATTCCTTGGATATACCAAGT...  ...  NaN      NaN   \n",
              "3       AGGTGAATGAAGAGACTAATGGGAGTGGCTTGCAAGCCAGGTACTG...  ...  NaN      NaN   \n",
              "4       CCATTGGCCCGCCCCAGTTGGCCGCAGGGACTGAGCAAGTTATGCG...  ...  NaN      NaN   \n",
              "...                                                   ...  ...  ...      ...   \n",
              "485571                                                NaN  ...  NaN      NaN   \n",
              "485572                                                NaN  ...  NaN      NaN   \n",
              "485573                                                NaN  ...  NaN      NaN   \n",
              "485574                                                NaN  ...  NaN      NaN   \n",
              "485575                                                NaN  ...  NaN      NaN   \n",
              "\n",
              "                 HMM_Island Regulatory_Feature_Name Regulatory_Feature_Group  \\\n",
              "0         Y:9973136-9976273                     NaN                      NaN   \n",
              "1                       NaN                     NaN                      NaN   \n",
              "2                       NaN                     NaN                      NaN   \n",
              "3                       NaN                     NaN                      NaN   \n",
              "4       Y:19697854-19699393                     NaN                      NaN   \n",
              "...                     ...                     ...                      ...   \n",
              "485571                  NaN                     NaN                      NaN   \n",
              "485572                  NaN                     NaN                      NaN   \n",
              "485573                  NaN                     NaN                      NaN   \n",
              "485574                  NaN                     NaN                      NaN   \n",
              "485575                  NaN                     NaN                      NaN   \n",
              "\n",
              "        DHS RANGE_START   RANGE_END     RANGE_GB    SPOT_ID  \n",
              "0       NaN   9363356.0   9363479.0  NC_000024.9        NaN  \n",
              "1       NaN  25314171.0  25314294.0  NC_000024.9        NaN  \n",
              "2       NaN  22741795.0  22741918.0  NC_000024.9        NaN  \n",
              "3       NaN  21664296.0  21664419.0  NC_000024.9        NaN  \n",
              "4       NaN  21239348.0  21239471.0  NC_000024.9        NaN  \n",
              "...     ...         ...         ...          ...        ...  \n",
              "485571  NaN         NaN         NaN          NaN  rs7746156  \n",
              "485572  NaN         NaN         NaN          NaN  rs1945975  \n",
              "485573  NaN         NaN         NaN          NaN   rs966367  \n",
              "485574  NaN         NaN         NaN          NaN   rs877309  \n",
              "485575  NaN         NaN         NaN          NaN  rs4331560  \n",
              "\n",
              "[485576 rows x 37 columns]"
            ]
          },
          "execution_count": 128,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "959bdb79-bac3-41cc-8f40-a954e1f26740"
      },
      "source": [
        "sites_descriptions = sites_descriptions.set_index('ID', drop = True)"
      ],
      "id": "959bdb79-bac3-41cc-8f40-a954e1f26740",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "d2039c00-2330-4801-927d-cef824d4deb1",
        "outputId": "df7b8d09-0577-4da0-86b8-f5d5e280c261"
      },
      "source": [
        "sites_descriptions.dtypes"
      ],
      "id": "d2039c00-2330-4801-927d-cef824d4deb1",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/plain": [
              "ID                              object\n",
              "Name                            object\n",
              "AddressA_ID                      int64\n",
              "AlleleA_ProbeSeq                object\n",
              "AddressB_ID                    float64\n",
              "AlleleB_ProbeSeq                object\n",
              "Infinium_Design_Type            object\n",
              "Next_Base                       object\n",
              "Color_Channel                   object\n",
              "Forward_Sequence                object\n",
              "Genome_Build                   float64\n",
              "CHR                             object\n",
              "MAPINFO                        float64\n",
              "SourceSeq                       object\n",
              "Chromosome_36                   object\n",
              "Coordinate_36                   object\n",
              "Strand                          object\n",
              "Probe_SNPs                      object\n",
              "Probe_SNPs_10                   object\n",
              "Random_Loci                     object\n",
              "Methyl27_Loci                   object\n",
              "UCSC_RefGene_Name               object\n",
              "UCSC_RefGene_Accession          object\n",
              "UCSC_RefGene_Group              object\n",
              "UCSC_CpG_Islands_Name           object\n",
              "Relation_to_UCSC_CpG_Island     object\n",
              "Phantom                         object\n",
              "DMR                             object\n",
              "Enhancer                        object\n",
              "HMM_Island                      object\n",
              "Regulatory_Feature_Name         object\n",
              "Regulatory_Feature_Group        object\n",
              "DHS                             object\n",
              "RANGE_START                    float64\n",
              "RANGE_END                      float64\n",
              "RANGE_GB                        object\n",
              "SPOT_ID                         object\n",
              "dtype: object"
            ]
          },
          "execution_count": 130,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "323f3eb8-bb20-43b1-8729-3069c61637cc",
        "outputId": "06de75ce-4b18-4d9f-88d9-39cb3d9e7112"
      },
      "source": [
        "sites_descriptions['UCSC_RefGene_Name'].value_counts()"
      ],
      "id": "323f3eb8-bb20-43b1-8729-3069c61637cc",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/plain": [
              "PTPRN2;PTPRN2;PTPRN2       1288\n",
              "MAD1L1;MAD1L1;MAD1L1        733\n",
              "PRDM16;PRDM16               623\n",
              "TNXB                        514\n",
              "DIP2C                       482\n",
              "                           ... \n",
              "MIR657;AATK                   1\n",
              "DDHD2;DDHD2                   1\n",
              "ANKS1B;FAM71C                 1\n",
              "SNORD114-11;SNORD114-10       1\n",
              "KRT26;KRT26                   1\n",
              "Name: UCSC_RefGene_Name, Length: 42438, dtype: int64"
            ]
          },
          "execution_count": 129,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "d09e5ebc-46ae-41a8-ab64-4e04d0d2c1f6"
      },
      "source": [
        "С каждым сайтом может быть ассоциировано несколько генов из-за альтернативного сплайсинга.\n",
        "Для целей анализа добавим столбец с  самым часто встречающиймся геном для каждого сайта."
      ],
      "id": "d09e5ebc-46ae-41a8-ab64-4e04d0d2c1f6"
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "19b4e522-7252-4d0f-94ba-f824fc37a47c"
      },
      "source": [
        "def most_common_element(list_genes):\n",
        "    return max(set(list_genes), key = list_genes.count)"
      ],
      "id": "19b4e522-7252-4d0f-94ba-f824fc37a47c",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "074e39a9-16c9-4799-9335-3e072488fc10"
      },
      "source": [
        "sites_with_genes = sites_descriptions[['UCSC_RefGene_Name']].dropna()"
      ],
      "id": "074e39a9-16c9-4799-9335-3e072488fc10",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "190df2fc-b6a1-4f2b-bc94-605a39b77332",
        "outputId": "1c88e329-d862-4209-f672-c56c7f63454a"
      },
      "source": [
        "sites_with_genes.shape"
      ],
      "id": "190df2fc-b6a1-4f2b-bc94-605a39b77332",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/plain": [
              "(365599, 1)"
            ]
          },
          "execution_count": 133,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "1308011d-ce56-4bf0-98a8-7c66a77ca34c"
      },
      "source": [
        "sites_with_genes['Most_Common_Gene']\\\n",
        "    = [most_common_element(x.split(';')) for x in sites_with_genes['UCSC_RefGene_Name']]"
      ],
      "id": "1308011d-ce56-4bf0-98a8-7c66a77ca34c",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "a936bb2c-766a-42ed-921b-8eb2486a9254"
      },
      "source": [
        "sites_descriptions = sites_descriptions.join(sites_with_genes[['Most_Common_Gene']], how = 'outer')"
      ],
      "id": "a936bb2c-766a-42ed-921b-8eb2486a9254",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "c4a5f661-34f5-4d3e-b729-8f2a9643f6c0",
        "outputId": "90e2d0e2-c88b-4c91-f6a6-d53f87ac61b0"
      },
      "source": [
        "sites_descriptions['Most_Common_Gene'].value_counts()"
      ],
      "id": "c4a5f661-34f5-4d3e-b729-8f2a9643f6c0",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/plain": [
              "PTPRN2       1299\n",
              "MAD1L1        733\n",
              "PRDM16        640\n",
              "TNXB          573\n",
              "DIP2C         490\n",
              "             ... \n",
              "PSMC5           1\n",
              "PPP3R2          1\n",
              "OR13F1          1\n",
              "KRTAP19-7       1\n",
              "MRPL2           1\n",
              "Name: Most_Common_Gene, Length: 20282, dtype: int64"
            ]
          },
          "execution_count": 137,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "4fd1eea9-bd8a-428b-ba89-f1addca1bb9f"
      },
      "source": [
        "sites_descriptions.to_csv(path_main_dir+\"\\\\GSE87571_preprocessed\\\\descriptions_sites.csv\")"
      ],
      "id": "4fd1eea9-bd8a-428b-ba89-f1addca1bb9f",
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "82e04533-7f4a-4e9c-aa9a-1a9befc1dfb0",
        "outputId": "a3d5878f-557e-4f9a-98f4-62a56bdd9cf3"
      },
      "source": [
        "sites_descriptions[sites_descriptions['Most_Common_Gene'].isna() == False].index"
      ],
      "id": "82e04533-7f4a-4e9c-aa9a-1a9befc1dfb0",
      "execution_count": null,
      "outputs": [
        {
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Name</th>\n",
              "      <th>AddressA_ID</th>\n",
              "      <th>AlleleA_ProbeSeq</th>\n",
              "      <th>AddressB_ID</th>\n",
              "      <th>AlleleB_ProbeSeq</th>\n",
              "      <th>Infinium_Design_Type</th>\n",
              "      <th>Next_Base</th>\n",
              "      <th>Color_Channel</th>\n",
              "      <th>Forward_Sequence</th>\n",
              "      <th>Genome_Build</th>\n",
              "      <th>...</th>\n",
              "      <th>Enhancer</th>\n",
              "      <th>HMM_Island</th>\n",
              "      <th>Regulatory_Feature_Name</th>\n",
              "      <th>Regulatory_Feature_Group</th>\n",
              "      <th>DHS</th>\n",
              "      <th>RANGE_START</th>\n",
              "      <th>RANGE_END</th>\n",
              "      <th>RANGE_GB</th>\n",
              "      <th>SPOT_ID</th>\n",
              "      <th>Most_Common_Gene</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>ID</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>cg00000029</th>\n",
              "      <td>cg00000029</td>\n",
              "      <td>14782418</td>\n",
              "      <td>AACTATACTAACRAAAAAATATCCAAAAAACACTAACRTATAAAAA...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>TTTTTTAGATAAGGATATCCAGGCGATGAGGAAGTTTTACTTCTGG...</td>\n",
              "      <td>37.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>16:53467838-53469685</td>\n",
              "      <td>Promoter_Associated</td>\n",
              "      <td>True</td>\n",
              "      <td>53468112.0</td>\n",
              "      <td>53468235.0</td>\n",
              "      <td>NC_000016.9</td>\n",
              "      <td>NaN</td>\n",
              "      <td>RBL2</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>cg00000108</th>\n",
              "      <td>cg00000108</td>\n",
              "      <td>12709357</td>\n",
              "      <td>ATACAATAAAACAAACCTAAAATAATCCTAACTCCRCTATCATCCT...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>TCCATTTTGAAGGAAAAAAATGAAGGCTCTGAAAGTGTAAATCGCT...</td>\n",
              "      <td>37.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>37459206.0</td>\n",
              "      <td>37459329.0</td>\n",
              "      <td>NC_000003.11</td>\n",
              "      <td>NaN</td>\n",
              "      <td>C3orf35</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>cg00000109</th>\n",
              "      <td>cg00000109</td>\n",
              "      <td>59755374</td>\n",
              "      <td>CAATACTAACAAACACATATACCCCCCCACAAATCTTAACTTCTAA...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>GCCTTAGTCCTGAATGAGCCATTTCTCTAAGAAGTCCTGGCTTCTT...</td>\n",
              "      <td>37.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>171916037.0</td>\n",
              "      <td>171916160.0</td>\n",
              "      <td>NC_000003.11</td>\n",
              "      <td>NaN</td>\n",
              "      <td>FNDC3B</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>cg00000236</th>\n",
              "      <td>cg00000236</td>\n",
              "      <td>12649348</td>\n",
              "      <td>TATAACRTCATATTAAAAAAAACRATCTAACCCACCAATTTATACA...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>CTCAGCGACAGTGTAGCGTCATGTTAGAGGAGACGATCTGACCCAC...</td>\n",
              "      <td>37.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>42263294.0</td>\n",
              "      <td>42263417.0</td>\n",
              "      <td>NC_000008.10</td>\n",
              "      <td>NaN</td>\n",
              "      <td>VDAC3</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>cg00000289</th>\n",
              "      <td>cg00000289</td>\n",
              "      <td>18766346</td>\n",
              "      <td>ATCTACTATATTCATTTCTCCAATCTCATATCCATTTTAATATAAA...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>CAAGTGAGCTAGCAAACACACATGCACCAATGTGCCTTTTGACAAG...</td>\n",
              "      <td>37.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>69341139.0</td>\n",
              "      <td>69341262.0</td>\n",
              "      <td>NC_000014.8</td>\n",
              "      <td>NaN</td>\n",
              "      <td>ACTN1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>ch.X.798879F</th>\n",
              "      <td>ch.X.798879F</td>\n",
              "      <td>37721346</td>\n",
              "      <td>GCACTTACAAACTATTTTAATTATTACCTCTTTTCCAAACTAAAAA...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>AGGTGTTGTTCTAGGTTTGGAGATAGAGCAGGGAGCAAAACAGAAA...</td>\n",
              "      <td>36.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>48341687.0</td>\n",
              "      <td>48341810.0</td>\n",
              "      <td>NC_000023.10</td>\n",
              "      <td>NaN</td>\n",
              "      <td>FTSJ1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>ch.X.881064F</th>\n",
              "      <td>ch.X.881064F</td>\n",
              "      <td>57635450</td>\n",
              "      <td>ACAACAACAAAATCCAAAATAATCACTCAAATTCCTTATAAACATA...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>AGAAGCTAAAGATATCGATAACAGCTCGTGGCAATTATATAACATA...</td>\n",
              "      <td>36.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>53673061.0</td>\n",
              "      <td>53673184.0</td>\n",
              "      <td>NC_000023.10</td>\n",
              "      <td>NaN</td>\n",
              "      <td>HUWE1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>ch.X.881546R</th>\n",
              "      <td>ch.X.881546R</td>\n",
              "      <td>32720319</td>\n",
              "      <td>TTCCAAATTTCCTATAAATCATAAATCCATTTATAATCAAATTTCC...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>GCCGCTGCACTCCAGCCTAGGTGACAGAATGAGACCCTGTTTCTTT...</td>\n",
              "      <td>36.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>53691005.0</td>\n",
              "      <td>53691128.0</td>\n",
              "      <td>NC_000023.10</td>\n",
              "      <td>NaN</td>\n",
              "      <td>HUWE1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>ch.X.938089F</th>\n",
              "      <td>ch.X.938089F</td>\n",
              "      <td>18739461</td>\n",
              "      <td>ATACCATACTAAAATATCCAACTCACCAAAACTTCCACCTACAATA...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>TGTATGTGGTATGAATCCAGTAACAAGATCTATGGCCGATCAAACA...</td>\n",
              "      <td>36.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>57358216.0</td>\n",
              "      <td>57358339.0</td>\n",
              "      <td>NC_000023.10</td>\n",
              "      <td>NaN</td>\n",
              "      <td>FAAH2</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>ch.X.967194F</th>\n",
              "      <td>ch.X.967194F</td>\n",
              "      <td>55686352</td>\n",
              "      <td>GACAATTAATTAAATTATAACAAATACATAACTCAAAATTACACAT...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>II</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>CAAGCCTAGATAACAGCCGTCTAGGCTTCATAGATAACAGCCATCT...</td>\n",
              "      <td>36.0</td>\n",
              "      <td>...</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>NaN</td>\n",
              "      <td>62695067.0</td>\n",
              "      <td>62695190.0</td>\n",
              "      <td>NC_000023.10</td>\n",
              "      <td>NaN</td>\n",
              "      <td>LOC92249</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>365599 rows × 37 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                      Name  AddressA_ID  \\\n",
              "ID                                        \n",
              "cg00000029      cg00000029     14782418   \n",
              "cg00000108      cg00000108     12709357   \n",
              "cg00000109      cg00000109     59755374   \n",
              "cg00000236      cg00000236     12649348   \n",
              "cg00000289      cg00000289     18766346   \n",
              "...                    ...          ...   \n",
              "ch.X.798879F  ch.X.798879F     37721346   \n",
              "ch.X.881064F  ch.X.881064F     57635450   \n",
              "ch.X.881546R  ch.X.881546R     32720319   \n",
              "ch.X.938089F  ch.X.938089F     18739461   \n",
              "ch.X.967194F  ch.X.967194F     55686352   \n",
              "\n",
              "                                               AlleleA_ProbeSeq  AddressB_ID  \\\n",
              "ID                                                                             \n",
              "cg00000029    AACTATACTAACRAAAAAATATCCAAAAAACACTAACRTATAAAAA...          NaN   \n",
              "cg00000108    ATACAATAAAACAAACCTAAAATAATCCTAACTCCRCTATCATCCT...          NaN   \n",
              "cg00000109    CAATACTAACAAACACATATACCCCCCCACAAATCTTAACTTCTAA...          NaN   \n",
              "cg00000236    TATAACRTCATATTAAAAAAAACRATCTAACCCACCAATTTATACA...          NaN   \n",
              "cg00000289    ATCTACTATATTCATTTCTCCAATCTCATATCCATTTTAATATAAA...          NaN   \n",
              "...                                                         ...          ...   \n",
              "ch.X.798879F  GCACTTACAAACTATTTTAATTATTACCTCTTTTCCAAACTAAAAA...          NaN   \n",
              "ch.X.881064F  ACAACAACAAAATCCAAAATAATCACTCAAATTCCTTATAAACATA...          NaN   \n",
              "ch.X.881546R  TTCCAAATTTCCTATAAATCATAAATCCATTTATAATCAAATTTCC...          NaN   \n",
              "ch.X.938089F  ATACCATACTAAAATATCCAACTCACCAAAACTTCCACCTACAATA...          NaN   \n",
              "ch.X.967194F  GACAATTAATTAAATTATAACAAATACATAACTCAAAATTACACAT...          NaN   \n",
              "\n",
              "             AlleleB_ProbeSeq Infinium_Design_Type Next_Base Color_Channel  \\\n",
              "ID                                                                           \n",
              "cg00000029                NaN                   II       NaN           NaN   \n",
              "cg00000108                NaN                   II       NaN           NaN   \n",
              "cg00000109                NaN                   II       NaN           NaN   \n",
              "cg00000236                NaN                   II       NaN           NaN   \n",
              "cg00000289                NaN                   II       NaN           NaN   \n",
              "...                       ...                  ...       ...           ...   \n",
              "ch.X.798879F              NaN                   II       NaN           NaN   \n",
              "ch.X.881064F              NaN                   II       NaN           NaN   \n",
              "ch.X.881546R              NaN                   II       NaN           NaN   \n",
              "ch.X.938089F              NaN                   II       NaN           NaN   \n",
              "ch.X.967194F              NaN                   II       NaN           NaN   \n",
              "\n",
              "                                               Forward_Sequence  Genome_Build  \\\n",
              "ID                                                                              \n",
              "cg00000029    TTTTTTAGATAAGGATATCCAGGCGATGAGGAAGTTTTACTTCTGG...          37.0   \n",
              "cg00000108    TCCATTTTGAAGGAAAAAAATGAAGGCTCTGAAAGTGTAAATCGCT...          37.0   \n",
              "cg00000109    GCCTTAGTCCTGAATGAGCCATTTCTCTAAGAAGTCCTGGCTTCTT...          37.0   \n",
              "cg00000236    CTCAGCGACAGTGTAGCGTCATGTTAGAGGAGACGATCTGACCCAC...          37.0   \n",
              "cg00000289    CAAGTGAGCTAGCAAACACACATGCACCAATGTGCCTTTTGACAAG...          37.0   \n",
              "...                                                         ...           ...   \n",
              "ch.X.798879F  AGGTGTTGTTCTAGGTTTGGAGATAGAGCAGGGAGCAAAACAGAAA...          36.0   \n",
              "ch.X.881064F  AGAAGCTAAAGATATCGATAACAGCTCGTGGCAATTATATAACATA...          36.0   \n",
              "ch.X.881546R  GCCGCTGCACTCCAGCCTAGGTGACAGAATGAGACCCTGTTTCTTT...          36.0   \n",
              "ch.X.938089F  TGTATGTGGTATGAATCCAGTAACAAGATCTATGGCCGATCAAACA...          36.0   \n",
              "ch.X.967194F  CAAGCCTAGATAACAGCCGTCTAGGCTTCATAGATAACAGCCATCT...          36.0   \n",
              "\n",
              "              ... Enhancer  HMM_Island Regulatory_Feature_Name  \\\n",
              "ID            ...                                                \n",
              "cg00000029    ...      NaN         NaN    16:53467838-53469685   \n",
              "cg00000108    ...      NaN         NaN                     NaN   \n",
              "cg00000109    ...      NaN         NaN                     NaN   \n",
              "cg00000236    ...      NaN         NaN                     NaN   \n",
              "cg00000289    ...      NaN         NaN                     NaN   \n",
              "...           ...      ...         ...                     ...   \n",
              "ch.X.798879F  ...      NaN         NaN                     NaN   \n",
              "ch.X.881064F  ...      NaN         NaN                     NaN   \n",
              "ch.X.881546R  ...      NaN         NaN                     NaN   \n",
              "ch.X.938089F  ...      NaN         NaN                     NaN   \n",
              "ch.X.967194F  ...      NaN         NaN                     NaN   \n",
              "\n",
              "             Regulatory_Feature_Group   DHS  RANGE_START    RANGE_END  \\\n",
              "ID                                                                      \n",
              "cg00000029        Promoter_Associated  True   53468112.0   53468235.0   \n",
              "cg00000108                        NaN   NaN   37459206.0   37459329.0   \n",
              "cg00000109                        NaN   NaN  171916037.0  171916160.0   \n",
              "cg00000236                        NaN   NaN   42263294.0   42263417.0   \n",
              "cg00000289                        NaN   NaN   69341139.0   69341262.0   \n",
              "...                               ...   ...          ...          ...   \n",
              "ch.X.798879F                      NaN   NaN   48341687.0   48341810.0   \n",
              "ch.X.881064F                      NaN   NaN   53673061.0   53673184.0   \n",
              "ch.X.881546R                      NaN   NaN   53691005.0   53691128.0   \n",
              "ch.X.938089F                      NaN   NaN   57358216.0   57358339.0   \n",
              "ch.X.967194F                      NaN   NaN   62695067.0   62695190.0   \n",
              "\n",
              "                  RANGE_GB SPOT_ID Most_Common_Gene  \n",
              "ID                                                   \n",
              "cg00000029     NC_000016.9     NaN             RBL2  \n",
              "cg00000108    NC_000003.11     NaN          C3orf35  \n",
              "cg00000109    NC_000003.11     NaN           FNDC3B  \n",
              "cg00000236    NC_000008.10     NaN            VDAC3  \n",
              "cg00000289     NC_000014.8     NaN            ACTN1  \n",
              "...                    ...     ...              ...  \n",
              "ch.X.798879F  NC_000023.10     NaN            FTSJ1  \n",
              "ch.X.881064F  NC_000023.10     NaN            HUWE1  \n",
              "ch.X.881546R  NC_000023.10     NaN            HUWE1  \n",
              "ch.X.938089F  NC_000023.10     NaN            FAAH2  \n",
              "ch.X.967194F  NC_000023.10     NaN         LOC92249  \n",
              "\n",
              "[365599 rows x 37 columns]"
            ]
          },
          "execution_count": 140,
          "metadata": {},
          "output_type": "execute_result"
        }
      ]
    }
  ]
}