removeSNPs {MethylSeekR} | R Documentation |
Removes CpGs that overlap with SNPs from methylation GRanges object.
removeSNPs(m, snps)
m |
GRanges object containing the methylation data. |
snps |
GRanges object containing the SNPs. |
The methylation GRanges object (m) with all CpGs overlapping SNPs removed.
Lukas Burger lukas.burger@fmi.ch
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)