CTSScoordinates: Genomic coordinates of TSSs from a 'CAGEr' object

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

Genomic coordinates of TSSs from a CAGEr object

Description

Extracts the genomic coordinates of all detected TSSs from CAGEexp objects.

Usage

CTSScoordinatesGR(object)

## S4 method for signature 'CAGEexp'
CTSScoordinatesGR(object)

CTSScoordinatesGR(object) <- value

## S4 replacement method for signature 'CAGEexp'
CTSScoordinatesGR(object) <- value

CTSStagCountSE(object) <- value

## S4 replacement method for signature 'CAGEexp'
CTSStagCountSE(object) <- value

Arguments

object	A CAGEexp object.
value	Coordinates to update, in a format according to the function name.

Value

CTSScoordinatesGR returns the coordinates as a CTSS() object wrapping genomic ranges. A filteredCTSSidx column metadata will be present if clusterCTSS() was ran earlier.

Author(s)

Vanja Haberle

Charles Plessy

See Also

getCTSS

clusterCTSS

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

Examples

CTSScoordinatesGR(exampleCAGEexp)

CTSScoordinatesGR(exampleCAGEexp)

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.