consensusClustersGR {CAGEr} | R Documentation

## 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.
`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 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.

`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)

[Package CAGEr version 2.0.2 Index]