methyAnalysis (version 1.14.0)

checkChrName: check chromosome names

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, RangedData object, character or named vector

addChr

Whether to add "chr" in front of chromosome names

Value

return the same type of object with chromosome names checked.

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).

Examples

data(exampleMethyGenoSet)
seqlevels(rowRanges(exampleMethyGenoSet))

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