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")