cumulativeCTSSdistribution {CAGEr} | R Documentation |
Calculates the cumulative sum of raw CAGE counts along each tag cluster or consensus cluster in every sample within a CAGEr object.
cumulativeCTSSdistribution( object, clusters = c("tagClusters", "consensusClusters"), useMulticore = FALSE, nrCores = NULL ) ## S4 method for signature 'CAGEr' cumulativeCTSSdistribution( object, clusters = c("tagClusters", "consensusClusters"), useMulticore = FALSE, nrCores = NULL )
object |
A |
clusters |
|
useMulticore |
Logical, should multicore be used.
|
nrCores |
Number of cores to use when |
In CAGEexp
objects, cumulative sums are stored
in the metadata slot using the RleList
class.
Vanja Haberle
Other CAGEr object modifiers:
CTSStoGenes()
,
CustomConsensusClusters()
,
aggregateTagClusters()
,
annotateCTSS()
,
clusterCTSS()
,
getCTSS()
,
normalizeTagCount()
,
quantilePositions()
,
summariseChrExpr()
Other CAGEr clusters functions:
CTSSclusteringMethod()
,
CTSScumulativesTagClusters()
,
CustomConsensusClusters()
,
aggregateTagClusters()
,
clusterCTSS()
,
consensusClustersDESeq2()
,
consensusClustersGR()
,
plotInterquantileWidth()
,
quantilePositions()
,
tagClustersGR()
CTSScumulativesTagClusters(exampleCAGEexp)[[1]][1:6] cumulativeCTSSdistribution(exampleCAGEexp, clusters = "consensusClusters") clusterCTSS( exampleCAGEexp, threshold = 50, thresholdIsTpm = TRUE , nrPassThreshold = 1, method = "distclu", maxDist = 20 , removeSingletons = TRUE, keepSingletonsAbove = 100) cumulativeCTSSdistribution(exampleCAGEexp, clusters = "tagClusters") aggregateTagClusters( exampleCAGEexp, tpmThreshold = 50 , excludeSignalBelowThreshold = FALSE, maxDist = 100) cumulativeCTSSdistribution(exampleCAGEexp, clusters = "consensusClusters")