CTSStagCountTable: Extracting CAGE tag count for TSSs 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 tag count for all detected TSSs in all CAGE datasets from CAGEset and CAGEexp objects.

Usage

CTSStagCountTable(object)

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

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

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

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

Arguments

object

A CAGEset or CAGEexp object.

Value

Returns an expression table with the number of CAGE tags supporting each TSS (rows) in every CAGE dataset (columns). The table is in data.frame format for CAGEset objects and in DataFrame format for CAGEexp objects. Use this function when the next consumer can handle both formats.

Author(s)

Vanja Haberle

See Also

getCTSS

Other CAGEr accessor methods: CTSSclusteringMethod, CTSScoordinates, CTSScumulativesTagClusters, CTSSnormalizedTpm, CTSStagCount, GeneExpDESeq2, GeneExpSE, consensusClustersGR, genomeName, inputFilesType, inputFiles, librarySizes, sampleLabels, seqNameTotalsSE, tagClusters

Examples

tagCount <- CTSStagCount(exampleCAGEset)
head(tagCount)

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