GenoSet-class: Class '"GenoSet"'

Description Extends Methods See Also Examples

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.

Methods

[

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"): ...

See Also

GenoSet

Examples

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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)

Bioconductor-mirror/genoset documentation built on July 1, 2017, 7:36 a.m.