GenoSet-class {genoset} | R Documentation

## 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.

### 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

    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)

[Package genoset version 1.42.0 Index]