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

In methyAnalysis: DNA methylation data analysis and visualization

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

Author(s)

Pan Du

See Also

filterBisulfiteVariant

Examples

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

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