cumulativeCTSSdistribution {CAGEr}

R Documentation

Cumulative sums of CAGE counts along genomic regions

Description

Calculates the cumulative sum of raw CAGE counts along each tag cluster or consensus cluster in every sample within a CAGEr object.

Usage

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
)

Arguments

object	A CAGEr object
clusters	tagClusters or consensusClusters.
useMulticore	Logical, should multicore be used. useMulticore = TRUE has no effect on non-Unix-like platforms.
nrCores	Number of cores to use when useMulticore = TRUE (set to NULL to use all detected cores).

Value

In CAGEexp objects, cumulative sums are stored in the metadata slot using the RleList class.

Author(s)

Vanja Haberle

See Also

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()

Examples

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")
           

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