inputFilesType {CAGEr} | R Documentation

## Input file formats for CAGEr objects

### Description

Get or set the information on the type of CAGE data input files from `CAGEset` and `CAGEexp` objects.

### Usage

    inputFilesType(object)

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

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

    inputFilesType(object) <- value

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

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

### Arguments

`object` | A CAGEset or CAGEexp object.
`value` | A character vector with one file type per sample.

### Details

The following input file types are supported:

- `bam`: A single-ended BAM file.

- `bamPairedEnd`: A paired-ended BAM file.

- `bed`: A BED file where each line counts for one molecule.

- `bedScore`: A BED file where the score indicates a number of counts for a given alignment

- `CAGEscanMolecule`: Experimental. For the CAGEscan 3.0 pipeline.

- `ctss`: A tabulation-delimited file describing CAGE Transcription Start Sites (CTSS) with four columns indicating chromosome, 1-based coordinate, strand and score respectively.

- `CTSStable`

- `FANTOM5`

- `ENCODE`

- `FANTOM3and4`

- `ZebrafishDevelopment`

### Value

Returns the type of the file format of CAGE data input files, e.g. `"bam"` or `"ctss"`. In the case of `CAGEexp` objects, the return value is character vector with one member per sample.

### Author(s)

Vanja Haberle

Charles Plessy

### See Also

`getCTSS`

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

Other CAGEr setter methods: `genomeName`, `inputFiles`, `sampleLabels`, `setColors`

### Examples

    inputFilesType(exampleCAGEset)

[Package CAGEr version 1.34.0 Index]