| savePMDSegments {MethylSeekR} | R Documentation |
Save PMD segments in rds format and as tab-delimited file.
savePMDSegments(PMDs, GRangesFilename, TableFilename)
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. |
No return value.
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)
#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")