removeWindow: Remove mutations that occuring at the same site

In benstory/mitoClone2: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Remove mutations that occuring at the same site

Description

Mutations co-occuring at the same genomic position may often be the result of sequencing artifacts or technical biases. In cases where the user which to drop these from a result this function may be used. ONLY WORKS FOR MITOCHONDRIAL MUTATIONS.

Usage

removeWindow(x, window = 1)

Arguments

x	A list of strings that comprise sites that will be filtered
window	Integer of how close mutations must be to one another (in bp) to be removed

Value

Returns the same list of mutations excluding those, if any, that fall within the same window =

Examples

P1.muts <- rep(TRUE,3)
names(P1.muts) <- c("X2537GA","X3351TC","X3350TC")
names(P1.muts) <- gsub("^X","",
gsub("(\\d+)([AGCT])([AGCT])","\\1 \\2>\\3",names(P1.muts)))
P1.muts <- P1.muts[removeWindow(names(P1.muts))]

benstory/mitoClone2 documentation built on Nov. 8, 2023, 12:13 a.m.