GenoSet-class {genoset} | R Documentation |
"GenoSet"
GenoSet
extends RangedSummarizedExperiment
by adding some
additional methods to the API. Examples include subsetting rows with a
GenomicRanges and combining this with access to assays like genoset[i,j,assay]
.
Class RangedSummarizedExperiment
, directly.
signature(x = "GenoSet", i = "ANY", j = "ANY", drop = "ANY")
: ...
signature(x = "GenoSet", i = "character", j = "ANY", drop = "ANY")
: ...
signature(x = "GenoSet", i = "ANY", j = "ANY", value = "ANY")
: ...
signature(object = "GenoSet")
: ...
signature(object = "GenoSet")
: ...
signature(object = "GenoSet")
: ...
signature(x = "GenoSet", y = "ANY")
: ...
signature(object = "GenoSet")
: ...
signature(x = "GenoSet")
: ...
signature(x = "GenoSet")
: ...
signature(x = "GenoSet")
: ...
signature(x = "GenoSet")
: ...
signature(object = "GenoSet")
: ...
signature(ds = "GenoSet")
: ...
signature(ds = "GenoSet")
: ...
signature(x = "GenoSet")
: ...
signature(x = "GenoSet", i="ANY")
: ...
signature(x = "GenoSet", i="ANY",value="ANY")
: ...
signature(x = "GenoSet")
: ...
signature(x = "GenoSet")
: ...
signature(x = "GenoSet")
: ...
signature(x = "GenoSet",value="GenomicRanges")
: ...
showClass("GenoSet") test.sample.names = LETTERS[11:13] probe.names = letters[1:10] assays=list(matrix(31:60,nrow=10,ncol=3,dimnames=list(probe.names,test.sample.names))) rowRanges=GRanges(ranges=IRanges(start=1:10,width=1,names=probe.names),seqnames=c(rep("chr1",4),rep("chr3",2),rep("chrX",4))) colData=data.frame(matrix(LETTERS[1:15],nrow=3,ncol=5,dimnames=list(test.sample.names,letters[1:5]))) rse=SummarizedExperiment(rowRanges=rowRanges,assays=assays,colData=colData,metadata=metadata) gs = GenoSet(rowRanges, assays, colData)