dot-get_3n_context_of_mutations: This function finds the tri-nucleotide context of mutations

In ActiveDriverWGS: A Driver Discovery Tool for Cancer Whole Genomes

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

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