| saveUMRLMRSegments {MethylSeekR} | R Documentation |
Save UMR and LMRs segments in rds format and/or as tab-delimited file
saveUMRLMRSegments(segs, GRangesFilename = NULL, TableFilename = NULL)
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. |
No return value. Only one filename is required.
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)
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")