CAGEr (version 1.14.0)

cumulativeCTSSdistribution: Calculating cumulative sum of CAGE signal along genomic region

Description

Calculates cumulative sum of CAGE signal along each tag cluster or consensus cluster in every CAGE dataset within CAGEset object.

Usage

cumulativeCTSSdistribution(object, clusters, useMulticore = FALSE,  nrCores = NULL)

Arguments

object

A CAGEset object

clusters

Which clusters should be used. Can be either clusters = "tagClusters" to calculate cumulative sum along tag clusters (different set of genomic coordinates for every CAGE experiment) or clusters = "consensusClusters" to calculate cumulative sum along consensus clusters (same set of genomic coordinates for every CAGE experiment).

useMulticore

Logical, should multicore be used. useMulticore = TRUE is supported only on Unix-like platforms.

nrCores

Number of cores to use when useMulticore = TRUE. Default value NULL uses all detected cores.

Value

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

Examples

load(system.file("data", "exampleCAGEset.RData", package="CAGEr"))

cumulativeCTSSdistribution(object = exampleCAGEset, clusters = "tagClusters")