extract_trinucleotide_context: Extracts the trinucleotide context for a set of mutations

Description Usage Arguments Value Examples

View source: R/extract_trinucleotide_context.R

Description

Extracts the trinucleotide context for a set of mutations

Usage

1

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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
)

alkodsi/ctDNAtools documentation built on Feb. 22, 2022, 9:40 a.m.