quantilePositions: Determine CTSS quantile positions within clusters

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

Determine CTSS quantile positions within clusters

Description

Calculates the positions of “upper” and “lower” quantiles of CAGE signal along tag clusters or consensus clusters in each sample of a CAGEexp object.

Usage

quantilePositions(
  object,
  clusters = c("tagClusters", "consensusClusters"),
  qLow = 0.1,
  qUp = 0.9,
  useMulticore = FALSE,
  nrCores = NULL
)

## S4 method for signature 'CAGEexp'
quantilePositions(
  object,
  clusters = c("tagClusters", "consensusClusters"),
  qLow = 0.1,
  qUp = 0.9,
  useMulticore = FALSE,
  nrCores = NULL
)

Arguments

object	A CAGEexp object.
clusters	Either tagClusters or consensusClusters.
qLow, qUp	Which “lower” or “upper” quantiles should be calculated. Numeric vector of values in range ⁠[0,1]⁠.
useMulticore	Logical, should multicore be used. useMulticore = TRUE has only effect on Unix-like platforms.
nrCores	Number of cores to use when useMulticore = TRUE. Default value NULL uses all detected cores.

Details

From the 5' end the position, the position of a quantile q is determined as the first base in which of the cumulative expression is higher or equal to q% of the total CAGE signal of that cluster. Promoter interquantile width is defined as the distance (in base pairs) between a “lower” and an “upper” quantile position.

Value

Returns the objects, in which the positions of the quantiles are defined relatively to the start point of their cluster, for more efficient Rle compression. The quantile data for tag clusters are stored in the TagClusters objects directly. The quantile data for ⁠consensus clusters⁠ are stored in integer matrices named “q_x”, where x represents the quantile (for instance, q_0.1), and these matrices are assays of the consensusClusters RangedSummarizedExperiment.

Author(s)

Vanja Haberle

Charles Plessy

See Also

Other CAGEr object modifiers: CTSStoGenes(), CustomConsensusClusters(), aggregateTagClusters(), annotateCTSS(), clusterCTSS(), cumulativeCTSSdistribution(), getCTSS(), normalizeTagCount(), quickEnhancers(), resetCAGEexp(), summariseChrExpr()

Other CAGEr clusters functions: CTSSclusteringMethod(), CTSScumulativesTagClusters(), CustomConsensusClusters(), aggregateTagClusters(), clusterCTSS(), consensusClustersDESeq2(), consensusClustersGR(), cumulativeCTSSdistribution(), plotInterquantileWidth(), tagClustersGR()

Examples

quantilePositions(exampleCAGEexp, "tagClusters",       qLow = c(0.1, 0.2), qUp = c(0.8, 0.9))
tagClustersGR(exampleCAGEexp)
quantilePositions(exampleCAGEexp, "consensusClusters", qLow = c(0.1, 0.2), qUp = c(0.8, 0.9))

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.