consensusClusters: Get consensus clusters from CAGEr objects

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

Get consensus clusters from CAGEr objects

Description

Extracts the information on consensus clusters from a CAGEr object.

Usage

consensusClustersGR(
  object,
  sample = NULL,
  returnInterquantileWidth = FALSE,
  qLow = NULL,
  qUp = NULL
)

## S4 method for signature 'CAGEexp'
consensusClustersGR(
  object,
  sample = NULL,
  returnInterquantileWidth = FALSE,
  qLow = NULL,
  qUp = NULL
)

consensusClustersSE(object)

## S4 method for signature 'CAGEexp'
consensusClustersSE(object)

Arguments

object	A CAGEr object.
sample	Optional. Label of the CAGE dataset (experiment, sample) for which to extract sample-specific information on consensus clusters. When no sample is specified (NULL), sample-agnostic information on consensus clusters is provided. This includes the dominant_ctss and tpm.dominant_ctss for each consensus cluster.
returnInterquantileWidth	Should the interquantile width of consensus clusters be returned? When sample argument is specified, the interquantile widths of the consensus clusters in that specified sample are returned, otherwise, the (sample-agnostic) interquantile width of the consensus cluster itself is returned.
qLow, qUp	Position of which quantile should be used as a left (lower) or right (upper) boundary when calculating interquantile width. Used only when returnInterquantileWidth = TRUE, otherwise ignored.

Value

consensusClustersGR returns a ConsensusClusters object, which wraps the GRanges class. The score columns indicates the normalised expression value of each cluster, either across all samples (sample = NULL), or for the selected sample. The legacy tpm column may be removed in the future. When sample argument is NOT specified, total CAGE signal across all CAGE datasets (samples) is returned in the tpm column. When sample argument is specified, the tpm column contains CAGE signal of consensus clusters in that specific sample. When returnInterquantileWidth = TRUE, additional sample-specific information is returned, including position of the dominant TSS, and interquantile width of the consensus clusters in the specified sample or otherwise, sample-agnostic information is returned.

consensusClustersSE returns the SummarizedExperiment stored in the consensusClusters experiment slot of the CAGEexp object.

Author(s)

Vanja Haberle

Charles Plessy

See Also

consensusClusters<-()

Other CAGEr accessor methods: CTSSclusteringMethod(), CTSScoordinatesGR(), CTSScumulativesTagClusters(), CTSSnormalizedTpmDF(), CTSStagCountDF(), GeneExpDESeq2(), GeneExpSE(), expressionClasses(), genomeName(), inputFilesType(), inputFiles(), librarySizes(), sampleLabels(), seqNameTotalsSE(), tagClustersGR()

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

Examples

consensusClustersGR( exampleCAGEexp, sample = 2
                   , returnInterquantileWidth = TRUE
                   , qLow = 0.1, qUp = 0.9)

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