MethylSeekR-package {MethylSeekR} | R Documentation

## Segmentation of Bis-seq methylation data

### Description

This is a package for the discovery of regulatory regions from Bis-seq data

### Details

Package: | MethylSeekR
Type: | Package
Version: | 1.0
Date: | 2012-10-10
License: | None

### Author(s)

Lukas Burger

Maintainer: Lukas Burger <Lukas.Burger@fmi.ch>

### References

Stadler, Murr, Burger et al, DNA-binding factors shape the mouse methylome at distal regulatory regions, Nature 2011.

### 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)

    #read SNP data
    snpFname <- system.file("extdata", "SNVs_hg18_chr22.tab",
    package="MethylSeekR")
    snps.gr <- readSNPTable(FileName=snpFname, seqLengths=sLengths)

    # remove SNPs
    meth.gr <- removeSNPs(meth.gr, snps.gr)

    #calculate alpha distribution for one chromosome
    plotAlphaDistributionOneChr(m=meth.gr, chr.sel="chr22", num.cores=1)

    #segment PMDs
    PMDsegments.gr <- segmentPMDs(m=meth.gr, chr.sel="chr22", num.cores=1,
    seqLengths=sLengths)

    #plot PMD segmentation examples
    plotPMDSegmentation(m=meth.gr, segs=PMDsegments.gr, numRegions=1)

    #save PMD segments
    savePMDSegments(PMDs=PMDsegments.gr, GRangesFilename="PMDs.gr.rds",
     TableFilename="PMDs.tab")

    #load CpG islands
    library(rtracklayer)
    session <- browserSession()
    genome(session) <- "hg18"
    query <- ucscTableQuery(session, "cpgIslandExt")
    CpGislands.gr <- track(query)
    genome(CpGislands.gr) <- NA
    CpGislands.gr <- resize(CpGislands.gr, 5000, fix="center")

    #calculate FDRs
    stats <- calculateFDRs(m=meth.gr, CGIs=CpGislands.gr,
    PMDs=PMDsegments.gr, num.cores=1)

    # select FDR cut-off and determine segmentation parameters
    FDR.cutoff <- 5
    m.sel <- 0.5
    n.sel=as.integer(names(stats$FDRs[as.character(m.sel), ]
    [stats$FDRs[as.character(m.sel), ]<FDR.cutoff])[1])

    #segment UMRs and LMRs
    UMRLMRsegments.gr <- segmentUMRsLMRs(m=meth.gr, meth.cutoff=m.sel,
    nCpG.cutoff=n.sel, PMDs=PMDsegments.gr, num.cores=1,
    myGenomeSeq=Hsapiens, seqLengths=sLengths)

    #plot final segmentation including PMDs, UMRs and LMRs
    plotFinalSegmentation(m=meth.gr, segs=UMRLMRsegments.gr, PMDs=PMDsegments.gr,
    meth.cutoff=m.sel, numRegions=1)

    #save UMRs and LMRs
    saveUMRLMRSegments(segs=UMRLMRsegments.gr, GRangesFilename="UMRsLMRs.gr.rds",
     TableFilename="UMRsLMRs.tab")

[Package MethylSeekR version 1.20.0 Index]