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 `CAGEexp` objects.

### Usage

    inputFilesType(object)

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

    inputFilesType(object) <- value

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

### Arguments

`object` | A 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()`, `CTSScoordinatesGR()`, `CTSScumulativesTagClusters()`, `CTSSnormalizedTpmDF()`, `CTSStagCountDF()`, `GeneExpDESeq2()`, `GeneExpSE()`, `consensusClustersGR()`, `expressionClasses()`, `genomeName()`, `inputFiles()`, `librarySizes()`, `sampleLabels()`, `seqNameTotalsSE()`, `tagClustersGR()`

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

### Examples

    inputFilesType(exampleCAGEexp)

[Package CAGEr version 2.0.2 Index]