expressionClasses: Extract labels of _expression classes_

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

Extract labels of expression classes

Description

Retrieves labels of expression classes of individual CTSSs or consensus clusters from a CAGEr object.

Usage

expressionClasses(object)

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

## S4 method for signature 'ConsensusClusters'
expressionClasses(object)

Arguments

object

A CAGEr object.

Value

Returns a Rle-encoded vector of labels of expression classes. The number of labels matches the number of expression clusters returned by getExpressionProfiles function.

See Also

Other CAGEr expression clustering functions: getExpressionProfiles(), plotExpressionProfiles()

Other CAGEr accessor methods: CTSScoordinatesGR(), CTSScumulativesTagClusters(), CTSSnormalizedTpmDF(), CTSStagCountDF(), GeneExpDESeq2(), GeneExpSE(), consensusClustersGR(), filteredCTSSidx(), genomeName(), inputFiles(), inputFilesType(), librarySizes(), sampleLabels(), seqNameTotalsSE(), tagClustersGR()

Examples

expressionClasses(CTSScoordinatesGR(exampleCAGEexp))
exampleCAGEexp |> consensusClustersGR() |> expressionClasses()

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