type_context: Retrieve context of base substitution types

In rayanramin/RamPack: Ramin's Package

Retrieve context of base substitution types

Description

A function to extract the bases 3' upstream and 5' downstream of the base substitution types. This function is from the MutationalPatterns Package.

Usage

type_context(vcf, ref_genome, extension = 1)

Arguments

vcf	A CollapsedVCF object
ref_genome	Reference genome
extension	The number of bases, that's extracted upstream and downstream of the base substitutions. (Default: 1).

Value

Mutation types and context character vectors in a named list

References

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0539-0

#' @export

rayanramin/RamPack documentation built on Sept. 2, 2023, 1:20 a.m.