subsetSmnvs: Subset for SNVs, DBSs, or indels

In UMCUGenetics/mutSigExtractor: Extracts SNV, indel, DBS, and SV signatures from vcf files.

Subset for SNVs, DBSs, or indels

Description

Standard variant filtering and subsetting for variant type used to clean the input dataframe for extractSigsSnv,Indel,Dbs() functions

Usage

subsetSmnvs(df, type, chrom.name.style = "UCSC", verbose = F)

Arguments

df	A dataframe containing the columns chrom, pos, ref, alt
type	Can be 'snv', 'indel', or 'dbs'
chrom.name.style	A string indicating the chromosome naming style. This can be for example 'UCSC' ('chrX') or 'NCBI' ('X'). See the documentation for 'GenomeInfoDb::seqlevelsStyle()' for more details.
verbose	Show progress messages?

Value

The filtered dataframe, or an empty dataframe if no variants exist/remain

UMCUGenetics/mutSigExtractor documentation built on Aug. 30, 2024, 2:12 p.m.