format_muts: This function filters hypermutated samples and returns the...

In ActiveDriverWGS: A Driver Discovery Tool for Cancer Whole Genomes

This function filters hypermutated samples and returns the formatted mutations with the appropriate trinucleotide context

Description

This function filters hypermutated samples and returns the formatted mutations with the appropriate trinucleotide context

Usage

format_muts(mutations, this_genome, filter_hyper_MB = NA)

Arguments

mutations	A data frame with the following columns: chr, pos1, pos2, ref, alt, patient chr autosomal chromosomes as chr1 to chr22 and sex chromosomes as chrX and chrY pos1 the start position of the mutation in base 1 coordinates pos2 the end position of the mutation in base 1 coordinates ref the reference allele as a string containing the bases A, T, C or G alt the alternate allele as a string containing the bases A, T, C or G patient the patient identifier as a string
this_genome	The reference genome object of BSgenome
filter_hyper_MB	The number of mutations per megabase for which a sample is considered hypermutated. Hypermutated samples will be removed in further analyses.

Value

a data frame called mutations which has been formatted with an extra column for trinucleotide context

Examples

data(cll_mutations)
this_genome = BSgenome.Hsapiens.UCSC.hg19::Hsapiens
formatted_mutations = format_muts(cll_mutations[1:10,], 
		filter_hyper_MB = 30, this_genome = this_genome)

ActiveDriverWGS documentation built on Sept. 3, 2022, 5:05 p.m.