mut_matrix_UI: Make mutation count matrix

In rayanramin/RamPack: Ramin's Package

Make mutation count matrix

Description

Make mutation count matrix this is a modification of the mut_matrix() function from MutationPatterns package

Usage

mut_matrix_UI(vcf_list, ref_genome, extension = 1, UI = FALSE)

Arguments

vcf_list	GRangesList or GRanges object.
ref_genome	BSgenome reference genome object
extension	The number of bases, that's extracted upstream and downstream of the base substitutions. (Default: 1).
UI	if set to TRUE the mean UI value will be calculated

Value

mutation count matrix

References

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

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