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 '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)

[Package CAGEr version 1.30.3 Index]