genomeName: Extracting genome name from CAGEr objects

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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 Oct. 27, 2024, 10:11 p.m.