CustomConsensusClusters: Expression levels of consensus cluster

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

Expression levels of consensus cluster

Description

Intersects custom consensus clusters with the CTSS data in a CAGEexp object, and stores the result as a expression matrices (raw and normalised tag counts).

Usage

CustomConsensusClusters(
  object,
  clusters,
  threshold = 0,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

## S4 method for signature 'CAGEexp,GRanges'
CustomConsensusClusters(
  object,
  clusters,
  threshold = 0,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

Arguments

object	A CAGEexp object
clusters	Consensus clusters in GRanges format.
threshold, nrPassThreshold	Only CTSSs with signal ⁠>= threshold⁠ in ⁠>= nrPassThreshold⁠ experiments will be used for clustering and will contribute towards total signal of the cluster.
thresholdIsTpm	Logical, is threshold raw tag count value (FALSE) or normalized signal (TRUE).

Details

Consensus clusters must not overlap, so that a single base of the genome can only be attributed to a single cluster. This is enforced by the .ConsensusClusters constructor.

Value

stores the result as a new RangedSummarizedExperiment in the experiment slot of the object. The assays of the new experiment are called counts and normalized. An outOfClusters column is added to the sample metadata to reflect the number of molecules that do not have their TSS in a consensus cluster.

Author(s)

Charles Plessy

See Also

Other CAGEr object modifiers: CTSStoGenes(), aggregateTagClusters(), annotateCTSS(), cumulativeCTSSdistribution(), distclu(), getCTSS(), normalizeTagCount(), paraclu(), quantilePositions(), quickEnhancers(), resetCAGEexp(), summariseChrExpr()

Other CAGEr clusters functions: CTSScumulativesTagClusters(), aggregateTagClusters(), consensusClustersDESeq2(), consensusClustersGR(), cumulativeCTSSdistribution(), distclu(), paraclu(), plotInterquantileWidth(), quantilePositions(), tagClustersGR()

Examples

cc <- consensusClustersGR(exampleCAGEexp)
CustomConsensusClusters(exampleCAGEexp, cc)

charles-plessy/CAGEr documentation built on Aug. 2, 2024, 4:35 p.m.