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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
MIT License
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switch ssm results from current to versioned results #46

Closed Kdreval closed 2 years ago

Kdreval commented 2 years ago

This implements a switch for SLMS-3 vcf2maf outputs from using flatfiles in _current directory to explicit 1.2 version. It returns identical output to the current implementation:

# get ssm from the master version, refers to files with _current
current_ssm = get_coding_ssm(from_flatfile = TRUE)
reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/slms-3_vcf2maf_current/level_3/final_merged_grch37.CDS.maf
mutations from 1428 samples
after linking with metadata, we have mutations from 1382 samples

dim(current_ssm)
[1] 163899     45

# get ssm from the version in this PR, refers explicitly to files in 1.2 directory
# confirm change is implemented
config::get("results_filatfiles")$ssm$all$cds
[1] "icgc_dart/slms_3-1.0_vcf2maf-1.2/level_3/final_merged_grch37.CDS.maf"

v1_2_ssm = get_coding_ssm(from_flatfile = TRUE)
reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/icgc_dart/slms_3-1.0_vcf2maf-1.2/level_3/final_merged_grch37.CDS.maf
mutations from 1428 samples
after linking with metadata, we have mutations from 1382 samples

dim(v1_2_ssm)
[1] 163899     45

# check that 2 ssms are the same and functionality is preserved
identical(current_ssm, v1_2_ssm)
[1] TRUE