consensusClusters: Get or set consensus clusters from CAGEr objects

Description Usage Arguments Value Author(s) See Also Examples

Description

Extracts the information on consensus clusters from a CAGEr object.

Usage

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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)

consensusClusters(object) <- value

## S4 replacement method for signature 'CAGEset'
consensusClusters(object) <- value

## S4 replacement method for signature 'CAGEexp'
consensusClusters(object) <- value

consensusClustersSE(object) <- value

## S4 replacement method for signature 'CAGEset,ANY'
consensusClustersSE(object) <- value


  ## S4 replacement method for signature 'CAGEexp,RangedSummarizedExperiment'
consensusClustersSE(object) <- value

consensusClustersGR(object) <- value

## S4 replacement method for signature 'CAGEset'
consensusClustersGR(object) <- value

## S4 replacement method for signature 'CAGEexp'
consensusClustersGR(object) <- value

consensusClustersSE(object) <- value

## S4 replacement method for signature 'CAGEset,ANY'
consensusClustersSE(object) <- value


  ## S4 replacement method for signature 'CAGEexp,RangedSummarizedExperiment'
consensusClustersSE(object) <- value

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

Position of which quantile should be used as a left (lower) boundary when calculating interquantile width. Used only when sample argument is specified and returnInterquantileWidth = TRUE, otherwise ignored.

qUp

Position of which quantile should be used as a right (upper) boundary when calculating interquantile width. Used only when sample argument is specified and returnInterquantileWidth = TRUE, otherwise ignored.

value

A data.frame of consensus clusters

Value

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

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

Examples

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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 May 2, 2018, 2:59 a.m.