supplement_maf.RdComplement maf with missing samples.
supplement_maf(incoming_maf, these_samples_metadata)The initial MAF data frame to be supplemented with missing samples.
The metadata data frame that contains Tumor_Sample_Barcode column with ids to be present in the complemented MAF.
maf_df with complemented Tumor_Sample_Barcode and other columns ready to be used downstream.
Specify the initial MAF with incoming_maf (to be supplemented with missing samples) and
give the function a filtered metadata table (with the sample IDs of interest) to the these_samples_metadata.
small_maf = get_coding_ssm(limit_cohort = "dlbcl_reddy",
seq_type = "capture")
#> reading from: /projects/nhl_meta_analysis_scratch/gambl/results_local/all_the_things/slms_3-1.0_vcf2maf-1.3/capture--projection/deblacklisted/augmented_maf/all_slms-3--grch37.CDS.maf
#> mutations from 2343 samples
#> after linking with metadata, we have mutations from 989 samples
small_maf = dplyr::filter(small_maf, Hugo_Symbol == "MYC")
my_metadata = get_gambl_metadata(seq_type_filter = "capture")
reddy_meta = dplyr::filter(my_metadata, cohort=="dlbcl_reddy")
complete_maf = supplement_maf(incoming_maf = small_maf,
these_samples_metadata = reddy_meta)