genomeName {CAGEr} | R Documentation

## Extracting genome name from CAGEr objects

### Description

Extracts the name of a referent genome from a `CAGEset` and `CAGEexp` objects.

### Usage

    genomeName(object)

    ## S4 method for signature 'CAGEset'
    genomeName(object)

    ## S4 method for signature 'CAGEexp'
    genomeName(object)

    ## S4 method for signature 'CTSS'
    genomeName(object)

    genomeName(object) <- value

    ## S4 replacement method for signature 'CAGEset'
    genomeName(object) <- value

    ## S4 replacement method for signature 'CAGEexp'
    genomeName(object) <- value

    ## S4 replacement method for signature 'CTSS'
    genomeName(object) <- value

### Arguments

`object` | A CAGEset or CAGEexp object.
`value` | The name of a `BSgenome` package.

### Details

`CAGEexp` objects constructed with `NULL` in place of the genome name can not run some commands that need access to genomic data, such as BigWig export or G-correction.

### Value

Returns a name of a BSgenome package used as a referent genome.

### Author(s)

Vanja Haberle

Charles Plessy

### See Also

Other CAGEr accessor methods: `CTSSclusteringMethod`, `CTSScoordinates`, `CTSScumulativesTagClusters`, `CTSSnormalizedTpm`, `CTSStagCountTable`, `CTSStagCount`, `GeneExpDESeq2`, `GeneExpSE`, `consensusClustersGR`, `inputFilesType`, `inputFiles`, `librarySizes`, `sampleLabels`, `seqNameTotalsSE`, `tagClusters`

Other CAGEr setter methods: `inputFilesType`, `inputFiles`, `sampleLabels`, `setColors`

### Examples

    genomeName(exampleCAGEset)

[Package CAGEr version 1.30.3 Index]