CTSScoordinates {CAGEr} | R Documentation

## Genomic coordinates of TSSs from a `CAGEr` object

### Description

Extracts the genomic coordinates of all detected TSSs from CAGEset and CAGEexp objects.

### Usage

    CTSScoordinates(object)

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

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

    CTSScoordinatesGR(object)

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

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

    CTSScoordinatesGR(object) <- value

    ## S4 replacement method for signature 'CAGEset'
    CTSScoordinatesGR(object) <- value

    ## S4 replacement method for signature 'CAGEexp'
    CTSScoordinatesGR(object) <- value

    CTSStagCountSE(object) <- value

    ## S4 replacement method for signature 'CAGEset'
    CTSStagCountSE(object) <- value

    ## S4 replacement method for signature 'CAGEexp'
    CTSStagCountSE(object) <- value

### Arguments

`object` | A `CAGEset` or `CAGEexp` object.
`value` | Coordinates to update, in a format according to the function name.

### Value

`CTSScoordinates()` returns a `data.frame` with genomic coordinates of all TSSs. The `pos` column contains 1-based coordinate of the TSS.

`CTSScoordinatesGR` returns the coordinates as a `CTSS()` object wrapping genomic ranges. A `filteredCTSSidx` column metadata will be present if `clusterCTSS()` was ran earlier.

### Author(s)

Vanja Haberle

Charles Plessy

### See Also

`getCTSS`

`clusterCTSS`

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

### Examples

    CTSS <- CTSScoordinates(exampleCAGEset)
    head(CTSS)

    CTSScoordinatesGR(exampleCAGEset)

[Package CAGEr version 1.30.3 Index]