methyAnalysis (version 1.14.0)

identifyCpG: Identify the CpG-site locations from a genome library

Description

Identify the CpG-site locations from a genome library

Usage

identifyCpG(bsgenome = "Hsapiens", seqnames, genomeLib = "BSgenome.Hsapiens.UCSC.hg19", pattern = "CG")

Arguments

bsgenome

a BSgenome object or variant name in the genomeLib

seqnames

chromosome names, if missing all chromosomes will be used.

genomeLib

the BSgenome library in Bioconductor

pattern

the sequence pattern to be matched.

Value

a GRanges object with CpG-site locations

See Also

filterBisulfiteVariant

Examples

  # library(GenomicFeatures)
  # library(BSgenome)
  # seqnames <- paste('chr', c(1:22, 'X', 'Y', 'M'), sep='')