CTSStagCountTable {CAGEr} | R Documentation

## Extracting CAGE tag count for TSSs from CAGEr objects

### Description

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

### Usage

    CTSStagCountTable(object)

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

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

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

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

### Arguments

`object` | A CAGEset or CAGEexp object.

### Value

Returns an expression table with the number of CAGE tags supporting each TSS (rows) in every CAGE dataset (columns). The table is in `data.frame` format for `CAGEset` objects and in `DataFrame` format for `CAGEexp` objects. Use this function when the next consumer can handle both formats.

### Author(s)

Vanja Haberle

### See Also

`getCTSS`

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

### Examples

    tagCount <- CTSStagCount(exampleCAGEset)
    head(tagCount)

[Package CAGEr version 1.34.0 Index]