inputFilesType {CAGEr} | R Documentation |
Get or set the information on the type of CAGE data input
files from CAGEexp
objects.
inputFilesType(object) ## S4 method for signature 'CAGEexp' inputFilesType(object) inputFilesType(object) <- value ## S4 replacement method for signature 'CAGEexp' inputFilesType(object) <- value
object |
A CAGEexp object. |
value |
A character vector with one file type per sample. |
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
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.
Vanja Haberle
Charles Plessy
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()
inputFilesType(exampleCAGEexp)