CTSSnormalizedTpm: Extracting normalized CAGE signal 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 normalized CAGE signal for all detected TSSs in all CAGE datasets from CAGEset and CAGEexp objects.

Usage

CTSSnormalizedTpm(object)

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

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

CTSSnormalizedTpmDf(object)

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

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

CTSSnormalizedTpmDF(object)

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

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

CTSSnormalizedTpmGR(object, samples)

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

Arguments

object	A CAGEset or CAGEexp object.
samples	The name of sample(s) as reported by sampleLabels(object), or the number identifying the sample(s).

Value

CTSSnormalizedTpm returns a data.frame containing coordinates and normalized CAGE signal supporting each TSS (rows) in every CAGE dataset (columns).

CTSSnormalizedTpmDf returns a data.frame of normalised expression values.

CTSSnormalizedTpmDF returns a DataFrame of normalised expression values.

Author(s)

Vanja Haberle

See Also

normalizeTagCount

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

Examples

head(CTSSnormalizedTpm(exampleCAGEset))

normalizeTagCount(exampleCAGEexp)
head(CTSSnormalizedTpm(exampleCAGEexp))

head(CTSSnormalizedTpmDf(exampleCAGEset))

normalizeTagCount(exampleCAGEexp)
head(CTSSnormalizedTpmDf(exampleCAGEexp))

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