inputFilesType: Input file formats for CAGEr objects

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.