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Updated final codes per discussion on OPC Issue 526 #350

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merged 10 commits into from
Apr 27, 2023
Merged

Updated final codes per discussion on OPC Issue 526 #350

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252acf6
Updated file as per discussion on OPC PR 526
sangeetashukla Apr 6, 2023
5ca5d61
Updated codes per discussion on OPC PR 350
sangeetashukla Apr 10, 2023
c289678
Updated with codes for new cancer_groups
sangeetashukla Apr 26, 2023
7881788
Added comment to describe purpose of the script
sangeetashukla Apr 26, 2023
585bfc6
Updated module TSVs to match and re-ran module for QC
sangeetashukla Apr 26, 2023
888760b
Updated to tidy up tab separation
sangeetashukla Apr 26, 2023
d14631b
Added cancer_group to gix QC issues
sangeetashukla Apr 26, 2023
30c0817
Other files after QC
sangeetashukla Apr 26, 2023
5b42871
Updated module with prefill from mol subtype integrate and re-run
sangeetashukla Apr 26, 2023
f4a487a
Updated EFO code for Wilms tumor to overwrite an obsolete one
sangeetashukla Apr 26, 2023
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5 changes: 5 additions & 0 deletions analyses/efo-mondo-mapping/01-merge-auto-search-ols-terms.R
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
# Author: Sangeeta Shukla (shuklas1@chop.edu)
# Purpose: This scripts automates the seach to retrieve EFO, MONDO, and NCIT ontology codes for all cancer_groups found in the histologies.tsv file.
# This reduces the manual work to only have to review the potential edge cases where the codes may not be perfect match for the cancer_groups.


# Load required libraries

suppressPackageStartupMessages({
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38 changes: 18 additions & 20 deletions analyses/efo-mondo-mapping/02-qc_efo_mondo_map.nb.html
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Expand Up @@ -1796,20 +1796,26 @@ <h2>Read efo-mondo-map.tsv and histologies file</h2>

histology_df &lt;- readr::read_tsv(file.path(integrate_dir, &quot;histologies.tsv&quot;), guess_max=100000)</code></pre>
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<pre><code>Parsed with column specification:
cols(
.default = col_character(),
age_at_diagnosis_days = col_double(),
OS_days = col_double(),
EFS_days = col_double(),
age_last_update_days = col_double(),
cns_methylation_class_score = col_double(),
cns_methylation_subclass_score = col_double(),
RF_purity_ABSOLUTE = col_double(),
RF_purity_ESTIMATE = col_double(),
RF_purity_LUMP = col_double(),
normal_fraction = col_double(),
tumor_fraction = col_double(),
tumor_ploidy = col_double()
tumor_ploidy = col_double(),
age_at_event_days = col_double(),
age_at_chemo_start = col_double(),
age_at_radiation_start = col_double(),
tumor_fraction_RFpurify_ABSOLUTE = col_double(),
tumor_fraction_RFpurify_ESTIMATE = col_double(),
tumor_fraction_LUMP = col_double(),
dkfz_v11_methylation_subclass_score = col_double(),
dkfz_v12_methylation_subclass_score = col_double(),
dkfz_v12_methylation_mgmt_estimated = col_double()
)</code></pre>
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Expand Down Expand Up @@ -1854,21 +1860,13 @@ <h2>Check to make sure all cancer groups in histologies are in efo mondo map fil
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<pre class="r"><code>cancer_group_effective[!cancer_group_effective %in% efo_mondo_map$cancer_group] </code></pre>
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<pre><code>[1] &quot;Pilocytic astrocytoma&quot; &quot;CNS Burkitt's lymphoma&quot;
[3] &quot;Diffuse fibrillary astrocytoma&quot; &quot;Gliosarcoma&quot;
[5] &quot;Neuroepithelial neoplasm&quot; </code></pre>
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<pre><code>[1] &quot;Supratentorial ependymoma&quot; &quot;Spinal ependymoma&quot; </code></pre>
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<pre><code>Pilocytic astrocytoma
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<pre><code>Supratentorial ependymoma

CNS Burkitt's lymphoma

Diffuse fibrillary astrocytoma

Gliosarcoma

Neuroepithelial neoplasm</code></pre>
Spinal ependymoma</code></pre>
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