saveUMRLMRSegments {MethylSeekR} | R Documentation

## Save UMR and LMR segments

### Description

Save UMR and LMRs segments in rds format and/or as tab-delimited file

### Usage

    saveUMRLMRSegments(segs, GRangesFilename = NULL, TableFilename = NULL)

### Arguments

`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.

### Value

No return value. Only one filename is required.

### Author(s)

Lukas Burger lukas.burger@fmi.ch

### 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)

    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")

[Package MethylSeekR version 1.30.0 Index]