Updated analysis: use annotator API in the rna-seq-expression-summary-stats module

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What analysis module should be updated and why?

The rna-seq-expression-summary-stats module should be updated to use the annotator API at analyses/long-format-table-utils/annotator/annotator-api.R, after

• PR [Long-format table annotation Part 2] annotator R API OpenPedCan-analysis#56 is merged

What changes need to be made? Please provide enough detail for another participant to make the update.

Use the long-format table annotator API in an analysis module with the following steps:

1. Change the working directory of the analysis module to be OpenPedCan-analysis or a subdirectory of OpenPedCan-analysis. This allows the API function annotate_long_format_table to locate annotation data files.
2. source the long-format-table-utils/annotator/annotator-api.R file.
3. If the class of the table to be annotated is not tibble::tbl_df, convert the table to tibble::tbl_df with tibble::as_tibble. After conversion, carefully check rownames, colnames, column classes (especially factors), and other properties that may affect the correctness of you code.
4. If c("Gene_symbol", "Gene_Ensembl_ID", "Disease") are not all present in the colnames of the table to be annotated, add new columns or rename existing ones to have all these required columns.
5. Call annotate_long_format_table to add one or more of the available annotation columns, by specifying the columns_to_add parameter in the annotate_long_format_table function. Read the documentation comment of the function for usage.
6. Rename, select, and reorder the columns of the annotated table for output in TSV, or JSON, or JSONL formats.

Following is an example usage in the rna-seq-expression-summary-stats module 01-tpm-summary-stats.R.

> getwd()
[1] "/home/rstudio/OpenPedCan-analysis/analyses/rna-seq-expression-summary-stats"
> source("../long-format-table-utils/annotator/annotator-api.R")
> class(m_tpm_ss_long_tbl)
[1] "tbl_df"     "tbl"        "data.frame"
> colnames(m_tpm_ss_long_tbl)
 [1] "gene_symbol"                          "gene_id"                             
 [3] "cancer_group"                         "cohort"                              
 [5] "tpm_mean"                             "tpm_sd"                              
 [7] "tpm_mean_cancer_group_wise_zscore"    "tpm_mean_gene_wise_zscore"           
 [9] "tpm_mean_cancer_group_wise_quantiles" "n_samples"                           
> renamed_m_tpm_ss_long_tbl <- dplyr::rename(
+   m_tpm_ss_long_tbl, Gene_symbol = gene_symbol, Gene_Ensembl_ID = gene_id,
+   Disease = cancer_group)
> annotated_renamed_m_tpm_ss_long_tbl <- annotate_long_format_table(
+   renamed_m_tpm_ss_long_tbl, columns_to_add = c("MONDO", "RMTL", "EFO"))
> m_tpm_ss_long_tbl <- dplyr::rename(
+   annotated_renamed_m_tpm_ss_long_tbl,
+   gene_symbol = Gene_symbol, gene_id = Gene_Ensembl_ID,
+   cancer_group = Disease)
> m_tpm_ss_long_tbl <- dplyr::select(
+   m_tpm_ss_long_tbl, gene_symbol, RMTL, gene_id,
+   cancer_group, EFO, MONDO, n_samples, cohort,
+   tpm_mean, tpm_sd,
+   tpm_mean_cancer_group_wise_zscore, tpm_mean_gene_wise_zscore,
+   tpm_mean_cancer_group_wise_quantiles)

What input data should be used? Which data were used in the version being updated?

• data/gene-expression-rsem-tpm-collapsed.rds
• data/histologies.tsv
• analyses/independent-samples/results/independent-specimens.rnaseq.primary.eachcohort.tsv

When do you expect the revised analysis will be completed?

1 day.

Who will complete the updated analysis?

@logstar

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Closed with PR d3b-center/OpenPedCan-analysis#64 merged.