MethylSeekR (version 1.12.0)

saveUMRLMRSegments: Save UMR and LMR segments

Description

Save UMR and LMRs segments in rds format and/or as tab-delimited file

Usage

saveUMRLMRSegments(segs, GRangesFilename = NULL, TableFilename = NULL)

Arguments

segs

GRanges object containing the UMR/LMR segmentation. Return value of the segmentUMRsLMRs function (see example).

GRangesFilename

Filename of the GRanges object.

TableFilename

Filename of the UMR/LMR table.

Value

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)

FDR.cutoff <- 5 
m.sel <- 0.5 
n.sel <- 3

#segment UMRs and LMRs, assuming no PMDs
UMRLMRsegments.gr <- segmentUMRsLMRs(m=meth.gr, meth.cutoff=m.sel,
nCpG.cutoff=n.sel, num.cores=1,
myGenomeSeq=Hsapiens, seqLengths=sLengths)

#save UMRs and LMRs
saveUMRLMRSegments(segs=UMRLMRsegments.gr, GRangesFilename="UMRsLMRs.gr.rds",
 TableFilename="UMRsLMRs.tab")