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)

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