CTSScoordinates {CAGEr}R Documentation

Genomic coordinates of TSSs from a CAGEr object

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)
[Package CAGEr version 1.29.2 Index]