CTSStagCount {CAGEr} | R Documentation

## Extract raw CAGE TSSs expression tables from `CAGEr` objects

### Description

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

### Usage

    CTSStagCount(object)

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

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

    CTSStagCountDf(object)

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

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

    CTSStagCountDF(object)

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

    CTSStagCountSE(object)

### Arguments

`object` | A `CAGEr` object.
`samples` | (For `CTSStagCountGR`.) Name(s) or number(s) identifying sample(s).

### 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:

- `CTSStagCount`: A `data.frame`, containing coordinates and expression values.

- `CTSStagCountDf`: A 'data.frame“, containing only expression values.

- `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.

### Author(s)

Vanja Haberle

Charles Plessy

### See Also

`getCTSS()`

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

### Examples

    head(CTSStagCount(exampleCAGEset))
    head(CTSStagCountDf(exampleCAGEset))
    CTSStagCountDF(exampleCAGEset)
    CTSStagCountDA(exampleCAGEset)

    head(CTSStagCount(exampleCAGEexp))
    head(CTSStagCountDf(exampleCAGEexp))
    CTSStagCountDF(exampleCAGEset)
    CTSStagCountDA(exampleCAGEset)

[Package CAGEr version 1.34.0 Index]