R: Get or set consensus clusters from CAGEr objects

consensusClustersGR {CAGEr}

R Documentation

Get or set 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 '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

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)

[Package CAGEr version 1.22.3 Index]