checkChrName: check chromosome names

In methyAnalysis: DNA methylation data analysis and visualization

Description

Check chromosome names and make sure chromosome names start with "chr" (or not if addChr is FALSE)

Usage

checkChrName(grange, addChr = TRUE)

Arguments

grange	a GRanges object, character or named vector
addChr	Whether to add "chr" in front of chromosome names

Details

Because some annotation database names the chromosomes without "chr" prefix, while many others do, it causes problems when both types of data exist in the analysis. This function aims to resolve such issues by checking chromosome names and make sure chromosome names start with "chr" (or not if addChr is FALSE).

Value

return the same type of object with chromosome names checked.

Author(s)

Pan Du

Examples

data(exampleMethyGenoSet)
seqlevels(rowRanges(exampleMethyGenoSet))

tt <- checkChrName(exampleMethyGenoSet, addChr = TRUE)
seqlevels(rowRanges(tt))

methyAnalysis documentation built on Nov. 8, 2020, 8:09 p.m.