gv_extr_mut_sig: gv_extr_mut_sig

In oriolarques/GEGVIC: A workflow to analyse Gene Expression, Genetic Variations and Immune cell Composition of tumour samples using Next Generation Sequencing data.

gv_extr_mut_sig

Description

Extracts mutational signatures contribution prediction from the deconstrucSigs package in a legible format.

Usage

gv_extr_mut_sig(results, ids_samples)

Arguments

results	Data frame containing the results of whichSignatures function from the deconstructSigs package.
ids_samples	Name of the samples of interest.

Value

Returns a data frame with the contribution of each mutational signature studied in each sample in a long format.

Examples

mut.sbs <- sample_mutations %>% dplyr::filter(Variant_Type == 'SNP')
sigs.sbs.input <- deconstructSigs::mut.to.sigs.input(
                                          mut.ref = mut.sbs,
                                          sample.id = 'Tumor_Sample_Barcode',
                                          chr = 'Chromosome',
                                          pos = 'Start_Position',
                                          ref = 'Reference_Allele',
                                          alt = 'Tumor_Seq_Allele2',
                                          bsg = BSgenome.Hsapiens.UCSC.hg38,
                                          sig.type = 'SBS')
ids_samples <- unique(sample_mutations$Tumor_Sample_Barcode)
results_sbs <- sapply(ids_samples,
                      function(x) {
                         deconstructSigs::whichSignatures(
                         tumor.ref = sigs.sbs.input,
                         signatures.ref = signatures.cosmic,
                         sample.id = x,
                         contexts.needed = TRUE,
                         tri.counts.method = 'default')
                     })

results_sbs.extr <- gv_extr_mut_sig(results_sbs)

oriolarques/GEGVIC documentation built on Oct. 30, 2024, 10:44 p.m.