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

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")

[Package CAGEr version 1.24.0 Index]