savePMDSegments: Save PMD segments

In MethylSeekR: Segmentation of Bis-seq data

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.

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)

#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")

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