extract_trinucleotide_context: Extracts the trinucleotide context for a set of mutations

In ctDNAtools: Analyze Circulating Tumor DNA Sequencing Data

Description

Extracts the trinucleotide context for a set of mutations

Usage

extract_trinucleotide_context(mutations, reference, destrand = TRUE)

Arguments

mutations	A data frame having the mutations. Should have the columns CHROM, POS, REF, ALT.
reference	the reference genome in BSgenome format
destrand	logical, whether to destrand mutations

Value

A data frame with two columns having the substitutions and the trinucleotide context

Examples

data("mutations", package = "ctDNAtools")
## Use human reference genome from BSgenome.Hsapiens.UCSC.hg19 library
suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))

## with destranding
extract_trinucleotide_context(mutations, BSgenome.Hsapiens.UCSC.hg19)

## without destranding
extract_trinucleotide_context(mutations, BSgenome.Hsapiens.UCSC.hg19,
  destrand = FALSE
)

ctDNAtools documentation built on March 26, 2020, 7:39 p.m.