consensusClusters: Get consensus clusters from CAGEr objects

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

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 'CAGEset'
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 'CAGEset'
consensusClustersSE(object)

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

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

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

Arguments

object	A CAGEr object.
sample	Optional. Label of the CAGE dataset (experiment, sample) for which to extract sample-specific information on consensus clusters.
returnInterquantileWidth	Should the interquantile width of consensus clusters in specified sample be returned. Used only when sample argument is specified, otherwise ignored.
qLow, qUp	Position of which quantile should be used as a left (lower) or right (upper) boundary when calculating interquantile width. Used only when sample argument is specified and returnInterquantileWidth = TRUE, otherwise ignored.

Value

consensusClustersGR returns a ConsensusClusters object, which is a GRanges wrapper containing similar information as the data frame returned by consensusClustersGR. The score columns indicates the normalised expression value of each cluster, either across all samples (sample = NULL), or for the selected sample. The tpm column provides the same information for compatibility with CAGEset objects but may be removed in the future.

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

consensusClusters returns a data.frame with information on consensus clusters, including genomic coordinates. 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.

Author(s)

Vanja Haberle

See Also

consensusClusters<-()

Other CAGEr accessor methods: CTSSclusteringMethod, CTSScoordinates, CTSScumulativesTagClusters, CTSSnormalizedTpm, CTSStagCountTable, CTSStagCount, GeneExpDESeq2, GeneExpSE, genomeName, inputFilesType, inputFiles, librarySizes, sampleLabels, seqNameTotalsSE, tagClusters

Other CAGEr clusters functions: CTSSclusteringMethod, CTSScumulativesTagClusters, CustomConsensusClusters, aggregateTagClusters, clusterCTSS, consensusClustersDESeq2, cumulativeCTSSdistribution, plotInterquantileWidth, quantilePositions, tagClusters

Examples

consensusClustersGR( exampleCAGEexp, sample = 2
                   , returnInterquantileWidth = TRUE
                   , qLow = 0.1, qUp = 0.9)
head(consensusClusters(exampleCAGEset))
head(consensusClusters(exampleCAGEset, sample = "sample2"))

cumulativeCTSSdistribution(exampleCAGEset, "consensusClusters") # Defaults in object do not fit
quantilePositions(exampleCAGEset, "consensusClusters")
head(consensusClusters(exampleCAGEset, sample = "sample2"
                      , returnInterquantileWidth = TRUE
                      , qLow = 0.1, qUp = 0.9))

head(consensusClusters(exampleCAGEexp))
consensusClustersGR(exampleCAGEexp, 2)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.