CTSStagCount {CAGEr}R Documentation

Extract raw CAGE TSSs expression tables from CAGEr objects

Description

Extracts the tag count for all detected TSSs in all CAGE datasets from CAGEset and CAGEexp objects.

Usage

CTSStagCount(object)

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

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

CTSStagCountDf(object)

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

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

CTSStagCountDF(object)

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

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

CTSStagCountDA(object)

## S4 method for signature 'CAGEr'
CTSStagCountDA(object)

CTSStagCountGR(object, samples)

## S4 method for signature 'CAGEr'
CTSStagCountGR(object, samples)

CTSStagCountSE(object)

Arguments

object

A CAGEr object.

samples

(For CTSStagCountGR.) Name(s) or number(s) identifying sample(s).

Value

Returns an object with number of CAGE tags supporting each TSS (rows) in every CAGE dataset (columns). The class of the object depends on the function being called:

Author(s)

Vanja Haberle

Charles Plessy

See Also

getCTSS()

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

Examples

head(CTSStagCount(exampleCAGEset))
head(CTSStagCountDf(exampleCAGEset))
CTSStagCountDF(exampleCAGEset)
CTSStagCountDA(exampleCAGEset)

head(CTSStagCount(exampleCAGEexp))
head(CTSStagCountDf(exampleCAGEexp))
CTSStagCountDF(exampleCAGEset)
CTSStagCountDA(exampleCAGEset)


[Package CAGEr version 1.30.3 Index]