genomeName: Extracting genome name from CAGEr objects

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

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)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.