genomeName {CAGEr} | R Documentation

## Extracting genome name from CAGEr objects

### Description

Extracts the name of a referent genome from a `CAGEexp` or a `CTSS` object.

### Usage

    genomeName(object)

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

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

    genomeName(object) <- value

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

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

### Arguments

`object` | A CAGEexp or a CTSS 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()`, `CTSScoordinatesGR()`, `CTSScumulativesTagClusters()`, `CTSSnormalizedTpmDF()`, `CTSStagCountDF()`, `GeneExpDESeq2()`, `GeneExpSE()`, `consensusClustersGR()`, `expressionClasses()`, `inputFilesType()`, `inputFiles()`, `librarySizes()`, `sampleLabels()`, `seqNameTotalsSE()`, `tagClustersGR()`

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

### Examples

    genomeName(exampleCAGEexp)

[Package CAGEr version 2.0.2 Index]