CTSStagCountDF {CAGEr} | R Documentation |
Extracts the tag count for all detected TSSs in all CAGE datasets
from CAGEexp
objects.
CTSStagCountDF(object) ## S4 method for signature 'CAGEexp' CTSStagCountDF(object) CTSStagCountDA(object) ## S4 method for signature 'CAGEr' CTSStagCountDA(object) CTSStagCountGR(object, samples) ## S4 method for signature 'CAGEexp' CTSStagCountGR(object, samples) CTSStagCountSE(object) ## S4 method for signature 'CAGEexp' CTSStagCountSE(object)
object |
A |
samples |
For |
Returns an object with number of CAGE tags supporting each TSS (rows) in every CAGE dataset (columns). The class of the object depends on the function being called:
CTSStagCountDA
: A DelayedArray
wrapping a DataFrame
of Rle
integers.
CTSStagCountSE
: A RangedSummarizedExperiment
containing a
DataFrameof
Rle' integers.
CTSStagCountGR
: A CTSS
object (wrapping GRanges
) containing a score
column indicating expression values for a given sample, or a
GRangesList
of CTSS
objects.
Vanja Haberle
Charles Plessy
Other CAGEr accessor methods:
CTSSclusteringMethod()
,
CTSScoordinatesGR()
,
CTSScumulativesTagClusters()
,
CTSSnormalizedTpmDF()
,
GeneExpDESeq2()
,
GeneExpSE()
,
consensusClustersGR()
,
expressionClasses()
,
genomeName()
,
inputFilesType()
,
inputFiles()
,
librarySizes()
,
sampleLabels()
,
seqNameTotalsSE()
,
tagClustersGR()
CTSStagCountDF(exampleCAGEexp) CTSStagCountDA(exampleCAGEexp) CTSStagCountGR(exampleCAGEexp, 1) CTSStagCountGR(exampleCAGEexp, "all") CTSStagCountSE(exampleCAGEexp)