GenoSet {genoset} | R Documentation

## Create a GenoSet object

### Description

This function is the preferred method for creating a new GenoSet object. Currently, a GenoSet is simply a RangedSummarizedExperiment with some API changes and extra methods. Therefore, a GenoSet must always have a rowRanges.

### Usage

    GenoSet(rowRanges, assays, colData, metadata = list())

    ## S4 method for signature 'GenoSet'
    lengths(x)

### Arguments

`rowRanges` | GenomicRanges, not a GenomicRangesList
`assays` | list, SimpleList or matrix-like object
`colData` | a data.frame or DataFrame of sample metadata with rownames matching the colnames of the matrices in assays
`metadata` | a list of any other data you want to attach to the GenoSet object
`x` | A GenoSet

### Details

locations. Rownames are required to match featureNames.

### Value

A GenoSet object

### Examples

    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 1.44.0 Index]