CTSSnormalizedTpm {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 `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))

[Package CAGEr version 1.30.3 Index]