Remove CpGs overlapping SNPs

Description

Removes CpGs that overlap with SNPs from methylation GRanges object.

Usage

removeSNPs(m, snps)

Arguments

Value

The methylation GRanges object (m) with all CpGs overlapping SNPs removed.

Author(s)

Lukas Burger lukas.burger@fmi.ch

Examples

library(MethylSeekR)

# get chromosome lengths
library("BSgenome.Hsapiens.UCSC.hg18")
sLengths=seqlengths(Hsapiens)

# read methylation data
methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",
package="MethylSeekR")
meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths)

#read SNP data
snpFname <- system.file("extdata", "SNVs_hg18_chr22.tab",
package="MethylSeekR")
snps.gr <- readSNPTable(FileName=snpFname, seqLengths=sLengths)

# remove SNPs
meth.gr <- removeSNPs(meth.gr, snps.gr)