CTSStagCount: Extract raw CAGE TSSs expression tables 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

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:

• CTSStagCount: A data.frame, containing coordinates and expression values.

• CTSStagCountDf: A 'data.frame“, containing only expression values.

• CTSStagCountDF: A DataFrame of Rle integers.

• CTSStagCountDA: A DelayedArray wrapping a DataFrame of Rle integers.

• CTSStagCountSE: A RangedSummarizedExperimentcontaining aDataFrameofRle' integers.

• CTSStagCountGR: A CTSS object (wrapping GRanges) containing a score column indicating expression values for a given sample.

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)

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