CTSSnormalizedTpm: Extracting normalized CAGE signal for TSSs from CAGEr objects

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Extracting normalized CAGE signal for TSSs from CAGEr objects

Description

Extracts the normalized CAGE signal for all detected TSSs in all CAGE datasets from CAGEexp objects.

Usage

CTSSnormalizedTpmDF(object)

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

CTSSnormalizedTpmGR(object, samples)

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

Arguments

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

Value

CTSSnormalizedTpmDF returns a DataFrame of normalised expression values.

Author(s)

Vanja Haberle

Charles Plessy

See Also

normalizeTagCount

Other CAGEr accessor methods: CTSScoordinatesGR(), CTSScumulativesTagClusters(), CTSStagCountDF(), GeneExpDESeq2(), GeneExpSE(), consensusClustersGR(), expressionClasses(), filteredCTSSidx(), genomeName(), inputFiles(), inputFilesType(), librarySizes(), sampleLabels(), seqNameTotalsSE(), tagClustersGR()

Examples

CTSSnormalizedTpmDF(exampleCAGEexp)

CTSSnormalizedTpmGR(exampleCAGEexp, 1)
exampleCAGEexp |> CTSSnormalizedTpmGR("all") 
 

charles-plessy/CAGEr documentation built on Oct. 27, 2024, 10:11 p.m.