selectByOverlap {methylKit} | R Documentation |
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
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)
object |
an |
ranges |
a GRanges object specifying the regions of interest |
a methylBase
,methylRaw
,
methylRawList
or methylDiff
object
depending on the input object.
Alexander Gosdschan
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)