CTSScoordinatesGR {CAGEr} | R Documentation

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

### Description

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

### Usage

    CTSScoordinatesGR(object)

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

    CTSScoordinatesGR(object) <- value

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

    CTSStagCountSE(object) <- value

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

### Arguments

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

### Value

`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()`, `CTSSnormalizedTpmDF()`, `CTSStagCountDF()`, `GeneExpDESeq2()`, `GeneExpSE()`, `consensusClustersGR()`, `expressionClasses()`, `genomeName()`, `inputFilesType()`, `inputFiles()`, `librarySizes()`, `sampleLabels()`, `seqNameTotalsSE()`, `tagClustersGR()`

### Examples

    CTSScoordinatesGR(exampleCAGEexp)

    CTSScoordinatesGR(exampleCAGEexp)

[Package CAGEr version 2.0.2 Index]