ActiveDriverWGS (version 1.2.0)

format_muts: 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)

Value

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

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.

Examples

# \donttest{
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)
# }