genomeName: Extracting genome name from CAGEr objects

genomeNameR 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: CTSScoordinatesGR(), CTSScumulativesTagClusters(), CTSSnormalizedTpmDF(), CTSStagCountDF(), GeneExpDESeq2(), GeneExpSE(), consensusClustersGR(), expressionClasses(), filteredCTSSidx(), inputFiles(), inputFilesType(), librarySizes(), sampleLabels(), seqNameTotalsSE(), tagClustersGR()

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

Examples

genomeName(exampleCAGEexp)


charles-plessy/CAGEr documentation built on Aug. 2, 2024, 4:35 p.m.