removeSNPs: Remove CpGs overlapping SNPs

In MethylSeekR: Segmentation of Bis-seq data

Description

Removes CpGs that overlap with SNPs from methylation GRanges object.

Usage

removeSNPs(m, snps)

Arguments

m	GRanges object containing the methylation data.
snps	GRanges object containing the SNPs.

Value

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

Author(s)

Lukas Burger [e-mail]

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)

MethylSeekR documentation built on Nov. 8, 2020, 6:57 p.m.