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

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 genomic coordinates of all detected TSSs from CAGEset and CAGEexp objects.

Usage

CTSScoordinates(object)

## S4 method for signature 'CAGEset'
CTSScoordinates(object)

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

CTSScoordinatesGR(object)

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

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

CTSScoordinatesGR(object) <- value

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

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

CTSStagCountSE(object) <- value

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

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

Arguments

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

Value

CTSScoordinates() returns a data.frame with genomic coordinates of all TSSs. The pos column contains 1-based coordinate of the TSS.

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, CTSSnormalizedTpm, CTSStagCountTable, CTSStagCount, GeneExpDESeq2, GeneExpSE, consensusClustersGR, genomeName, inputFilesType, inputFiles, librarySizes, sampleLabels, seqNameTotalsSE, tagClusters

Examples

CTSS <- CTSScoordinates(exampleCAGEset)
head(CTSS)

CTSScoordinatesGR(exampleCAGEset)

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