genoset (version 1.28.2)

GenoSet-class: Class "GenoSet"

Description

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].

Extends

Class RangedSummarizedExperiment, directly.

See Also

GenoSet

Examples

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)