.get_3n_context_of_mutations {ActiveDriverWGS}R Documentation

This function finds the tri-nucleotide context of mutations

Description

This function finds the tri-nucleotide context of mutations

Usage

.get_3n_context_of_mutations(mutations, this_genome)

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, for example BSgenome.Hsapiens.UCSC.hg19::Hsapiens

Value

A data frame consisting of the same columns as the original mutations data frame and sorted by SNVs and Indels with an additional column tag which indicates the trinucleotide context of the mutation


[Package ActiveDriverWGS version 1.1.2 Index]