GenoSet-class: Class '"GenoSet"'
In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description Extends Methods See Also Examples

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"): ...
chr: signature(object = "GenoSet"): ...
chrNames: signature(object = "GenoSet"): ...
dim: signature(object = "GenoSet"): ...
genoPlot: signature(x = "GenoSet", y = "ANY"): ...
rowRanges: signature(object = "GenoSet"): ...
names: signature(x = "GenoSet"): ...
ranges: signature(x = "GenoSet"): ...
chrInfo: signature(x = "GenoSet"): ...
chrIndices: signature(x = "GenoSet"): ...
show: signature(object = "GenoSet"): ...
toGenomeOrder: signature(ds = "GenoSet"): ...
isGenomeOrder: signature(ds = "GenoSet"): ...
assays: signature(x = "GenoSet"): ...
assay: signature(x = "GenoSet", i="ANY"): ...
assay<-: signature(x = "GenoSet", i="ANY",value="ANY"): ...
assayNames: signature(x = "GenoSet"): ...
colData: signature(x = "GenoSet"): ...
locData: signature(x = "GenoSet"): ...
locData<-: signature(x = "GenoSet",value="GenomicRanges"): ...

GenoSet

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)