selectByOverlap {methylKit} | R Documentation

## selects records of methylDB objects lying inside a GRanges range

### Description

The function selects records from any `methylKit` object that lie inside the regions given by `ranges` of class `GRanges` and returns an in-memory equivalent of this object

### Usage

    selectByOverlap(object,ranges)

    ## S4 method for signature 'methylRaw,GRanges'
    selectByOverlap(object, ranges)

    ## S4 method for signature 'methylRawList,GRanges'
    selectByOverlap(object, ranges)

    ## S4 method for signature 'methylBase,GRanges'
    selectByOverlap(object, ranges)

    ## S4 method for signature 'methylDiff,GRanges'
    selectByOverlap(object, ranges)

    ## S4 method for signature 'methylRawDB,GRanges'
    selectByOverlap(object, ranges)

    ## S4 method for signature 'methylRawListDB,GRanges'
    selectByOverlap(object, ranges)

    ## S4 method for signature 'methylBaseDB,GRanges'
    selectByOverlap(object, ranges)

    ## S4 method for signature 'methylDiffDB,GRanges'
    selectByOverlap(object, ranges)

### Arguments

`object` | an `methylRaw`,`methylRawDB`, `methylRawList`, `methylRawListDB`, `methylBase`, `methylBaseDB`, `methylDiff` or `methylDiffDB` object
`ranges` | a GRanges object specifying the regions of interest

### Value

a `methylBase`,`methylRaw`, `methylRawList` or `methylDiff` object depending on the input object.

### Author(s)

Alexander Gosdschan

### Examples

    data(methylKit)

    file.list=list( system.file("extdata", "test1.myCpG.txt", package = "methylKit"),
                    system.file("extdata", "test2.myCpG.txt", package = "methylKit"),
                    system.file("extdata", "control1.myCpG.txt", package = "methylKit"),
                    system.file("extdata", "control2.myCpG.txt", package = "methylKit") )

    methylRawListDB.obj=methRead(file.list,
                             sample.id=list("test1","test2","ctrl1","ctrl2"),
                             assembly="hg18",treatment=c(1,1,0,0),
                             dbtype = "tabix",dbdir = "methylDB")

    methylBaseDB.obj=unite(methylRawListDB.obj)

    methylDiffDB.obj = calculateDiffMeth(methylBaseDB.obj)

    # define the windows of interest as a GRanges object, this can be any set
    # of genomic locations
    library(GenomicRanges)
    my.win=GRanges(seqnames="chr21",
    ranges=IRanges(start=seq(from=9764513,by=10000,length.out=20),width=5000) )

    # selects the records that lie inside the regions
    myRaw <- selectByOverlap(methylRawListDB.obj[[1]],my.win)

    # selects the records that lie inside the regions
    myBase <- selectByOverlap(methylBaseDB.obj,my.win)

    # selects the records that lie inside the regions
    myDiff <- selectByOverlap(methylDiffDB.obj,my.win)

    # selects the records that lie inside the regions
    myRaw2 <- selectByOverlap(methylRawList.obj[[1]],my.win)

    # selects the records that lie inside the regions
    myRawList2 <- selectByOverlap(methylRawList.obj,my.win)

    # selects the records that lie inside the regions
    myBase2 <- selectByOverlap(methylBase.obj,my.win)

    # selects the records that lie inside the regions
    myDiff2 <- selectByOverlap(methylDiff.obj,my.win)

    rm(methylRawListDB.obj)
    rm(methylBaseDB.obj)
    rm(methylDiffDB.obj)
    unlink("methylDB",recursive=TRUE)

[Package methylKit version 1.12.0 Index]