CTSSnormalizedTpmDF {CAGEr}

R Documentation

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: CTSSclusteringMethod(), CTSScoordinatesGR(), CTSScumulativesTagClusters(), CTSStagCountDF(), GeneExpDESeq2(), GeneExpSE(), consensusClustersGR(), expressionClasses(), genomeName(), inputFilesType(), inputFiles(), librarySizes(), sampleLabels(), seqNameTotalsSE(), tagClustersGR()

Examples

CTSSnormalizedTpmDF(exampleCAGEexp)

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

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