CTSStagCountDF {CAGEr} | R Documentation

## Raw CAGE TSSs expression counts

### Description

Extracts the tag count for all detected TSSs in all CAGE datasets from `CAGEexp` objects.

### Usage

    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 'CAGEexp'
    CTSStagCountGR(object, samples)

    CTSStagCountSE(object)

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

### Arguments

`object` | A `CAGEexp` object.
`samples` | For `CTSStagCountGR` only: name(s) or number(s) identifying sample(s) or "all" to return a `GRangesList` of all the samples.

### 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:

- `CTSStagCountDF`: A `DataFrame` of `Rle` integers.

- `CTSStagCountDA`: A `DelayedArray` wrapping a `DataFrame` of `Rle` integers.

- `CTSStagCountSE`: A `RangedSummarizedExperiment` `containing a`DataFrame`of`Rle' integers.

- `CTSStagCountGR`: A `CTSS` object (wrapping `GRanges`) containing a `score` column indicating expression values for a given sample, or a `GRangesList` of `CTSS` objects.

### Author(s)

Vanja Haberle

Charles Plessy

### See Also

`getCTSS()`

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

### Examples

    CTSStagCountDF(exampleCAGEexp)

    CTSStagCountDA(exampleCAGEexp)

    CTSStagCountGR(exampleCAGEexp, 1)
    CTSStagCountGR(exampleCAGEexp, "all")

    CTSStagCountSE(exampleCAGEexp)

[Package CAGEr version 2.0.2 Index]