CTSStagCount {CAGEr} | R Documentation |
CAGEr
objectsExtracts the tag count for all detected TSSs in all CAGE datasets
from CAGEset
and CAGEexp
objects.
CTSStagCount(object) ## S4 method for signature 'CAGEset' CTSStagCount(object) ## S4 method for signature 'CAGEexp' CTSStagCount(object) CTSStagCountDf(object) ## S4 method for signature 'CAGEset' CTSStagCountDf(object) ## S4 method for signature 'CAGEexp' CTSStagCountDf(object) CTSStagCountDF(object) ## S4 method for signature 'CAGEset' 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 'CAGEr' CTSStagCountGR(object, samples) 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:
CTSStagCount
: A data.frame
, containing coordinates and expression values.
CTSStagCountDf
: A 'data.frame“, containing only expression values.
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.
Vanja Haberle
Charles Plessy
Other CAGEr accessor methods: CTSSclusteringMethod
,
CTSScoordinates
,
CTSScumulativesTagClusters
,
CTSSnormalizedTpm
,
CTSStagCountTable
,
GeneExpDESeq2
, GeneExpSE
,
consensusClustersGR
,
genomeName
, inputFilesType
,
inputFiles
, librarySizes
,
sampleLabels
,
seqNameTotalsSE
, tagClusters
head(CTSStagCount(exampleCAGEset)) head(CTSStagCountDf(exampleCAGEset)) CTSStagCountDF(exampleCAGEset) CTSStagCountDA(exampleCAGEset) head(CTSStagCount(exampleCAGEexp)) head(CTSStagCountDf(exampleCAGEexp)) CTSStagCountDF(exampleCAGEset) CTSStagCountDA(exampleCAGEset)