cumulativeCTSSdistribution: Cumulative sums of CAGE counts along genomic regions

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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

For CAGEset objects, the slot CTSScumulativesTagClusters (when clusters = "tagClusters") or CTSScumulativesConsensusClusters (when clusters = "consensusClusters") of the will be occupied by the list containing cumulative sum of the CAGE signal along genomic regions per CAGE experiment. 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, tagClusters

Examples

CTSScumulativesTagClusters(exampleCAGEset)[[1]][1:6]
cumulativeCTSSdistribution(object = exampleCAGEset, clusters = "tagClusters")
CTSScumulativesTagClusters(exampleCAGEset)[[1]][1:6]
cumulativeCTSSdistribution(exampleCAGEset, 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")
           

CAGEr documentation built on Jan. 17, 2021, 2 a.m.