Updated analysis: use annotator CLI in the cnv-frequencies module

[logstar]

What analysis module should be updated and why?

The cnv-frequencies module should be updated to use the annotator CLI at analyses/long-format-table-utils/annotator/annotator-api.R, after

• PR [Long-format table annotation Part 3] annotator R CLI OpenPedCan-analysis#59 is merged

(EDIT 07/26/2021 YZ: removed the requirement to merge d3b-center/OpenPedCan-analysis#52 before working on this issue)

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

Remove annotation related code in analyses/cnv-frequencies/01-cnv-frequencies.py.

Use the long-format table annotator CLI in the cnv-frequencies module with the following steps:

1. If "Gene_symbol", "Gene_Ensembl_ID", "Disease" (case-sensitive) are not all present in the column names of the table to be annotated, add new columns or rename existing ones to have all these required columns.
2. Output the table that needs to be annotated in TSV format.
3. Make sure that the working directory is OpenPedCan-analysis or a subdirectory of OpenPedCan-analysis. This allows the annotator-cli.R to locate the annotator-api.R.
4. Run the annotator-cli.R script with Rscript --vanilla path/to/annotator-cli.R and proper options. The Rscript command can be invoked by Python (>= 3.5) import subprocess; subprocess.run("Rscript --vanilla analyses/long-format-table-utils/annotator/annotator-cli.R -h".split()). For more information about Python (>= 3.5) subprocess.run, https://docs.python.org/3/library/subprocess.html#subprocess.run.
5. Read the annotated table TSV file.
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"
> 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)
> 
> readr::write_tsv(
+   renamed_m_tpm_ss_long_tbl,
+   "../../scratch/renamed_m_tpm_ss_long_tbl.tsv")
> 
> system(paste(
+   "Rscript --vanilla ../long-format-table-utils/annotator/annotator-cli.R",
+   "-r -v -c MONDO,RMTL,EFO",
+   "-i ../../scratch/renamed_m_tpm_ss_long_tbl.tsv",
+   "-o ../../scratch/annotated_renamed_m_tpm_ss_long_tbl.tsv"))
Read ../../scratch/renamed_m_tpm_ss_long_tbl.tsv...
Annotate ../../scratch/renamed_m_tpm_ss_long_tbl.tsv...
Output ../../scratch/annotated_renamed_m_tpm_ss_long_tbl.tsv...
Done.
> 
> annotated_renamed_m_tpm_ss_long_tbl <- readr::read_tsv(
+   "../../scratch/annotated_renamed_m_tpm_ss_long_tbl.tsv",
+   na = character(),
+   col_types = readr::cols(.default = readr::col_guess()))
|==================================================================================================| 100%  222 MB
> 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/histologies.tsv
• data/consensus_seg_annotated_cn_autosomes.tsv.gz
• data/consensus_seg_annotated_cn_x_and_y.tsv.gz
• analyses/independent-samples/results/independent-specimens.wgs.primary.eachcohort.tsv
• analyses/independent-samples/results/independent-specimens.wgs.relapse.eachcohort.tsv

When do you expect the revised analysis will be completed?

1-2 days.

Who will complete the updated analysis?

@ewafula

[logstar]

@ewafula The annotator CLI is merged to the dev branch, so it could be used for your CNV module now.

[ewafula]

Thanks, @logstar. I Will start working to update the CNV module immediately.

…

On Mon, Jul 26, 2021 at 11:06 AM Yuanchao Zhang ***@***.***> wrote: @ewafula <https://github.com/ewafula> The annotator CLI is merged to the dev branch <d3b-center/OpenPedCan-analysis#59>, so it could be used for your CNV module now. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#124 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZN26CB3EJCQDK4QDJYXLLTZV2XJANCNFSM5AWHVLNA> .

[ewafula]

@logstar, the long-format-table-utils analysis module annotator might need updating with input files from v7. Works ok with updated CNV module with v6 but not v7. Checked my local branch is up to date.

root@ab9dc5db917d:/home/OpenPedCan-analysis# bash analyses/cnv-frequencies/run-cnv-frequencies-analysis.sh                               
Read analyses/cnv-frequencies/results/consensus_wgs_plus_cnvkit_wxs_autosomes_freq.tsv...                                                                                                  
Annotate analyses/cnv-frequencies/results/consensus_wgs_plus_cnvkit_wxs_autosomes_freq.tsv...                                            
Error: '/home/OpenPedCan-analysis/data/ensg-hugo-rmtl-v1-mapping.tsv' does not exist.                                                                                                      
Execution halted 

[logstar]

@ewafula Thank you for checking. This will be fixed in d3b-center/OpenPedCan-analysis#66. You could adapt the changes of analyses/long-format-table-utils/annotator/annotator-api.R in your local branch without committing to use it for v7.

[logstar]

Closed with PR d3b-center/OpenPedCan-analysis#52 merged.