MethylSeekR (version 1.12.0)

savePMDSegments: Save PMD segments

Description

Save PMD segments in rds format and as tab-delimited file.

Usage

savePMDSegments(PMDs, GRangesFilename, TableFilename)

Arguments

PMDs

GRanges object containing the PMD segmentation. Return value of the segmentPMDs function (see example).

GRangesFilename

Filename of the GRanges object.

TableFilename

Filename of the PMD table.

Value

No return 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)

#segment PMDs
PMDsegments.gr <- segmentPMDs(m=meth.gr, chr.sel="chr22",
seqLengths=sLengths)

#save PMD segments
savePMDSegments(PMDs=PMDsegments.gr, GRangesFilename="PMDs.gr.rds",
 TableFilename="PMDs.tab")