tagClustersGR {CAGEr} | R Documentation

## Extract tag clusters (TCs) for individual CAGE experiments

### Description

Extracts tag clusters (TCs) produced by `clusterCTSS` function for a specified CAGE experiment from a `CAGEexp` object.

### Usage

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

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

    tagClustersGR(object, sample = NULL) <- value

    ## S4 replacement method for signature 'CAGEexp,ANY,TagClusters'
    tagClustersGR(object, sample = NULL) <- value

    ## S4 replacement method for signature 'CAGEexp,missing,GRangesList'
    tagClustersGR(object, sample = NULL) <- value

### Arguments

`object` | A `CAGEexp` object.
`sample` | Label of the CAGE dataset (experiment, sample) for which to extract tag clusters. If `samples = NULL`, a list of all the clusters for each sample is returned.
`returnInterquantileWidth` | Return the interquantile width for each tag cluster.
`qLow, qUp` | Position of which quantile should be used as a left (lower) or right (upper) boundary (for `qLow` and `qUp` respectively) when calculating interquantile width. Default value `NULL` results in using the start coordinate of the cluster. Used only when `returnInterquantileWidth = TRUE`, otherwise ignored.
`value` | A `TagClusters` object.

### Value

Returns a `GRangesList` or a `GRanges` object with genomic coordinates, position of dominant TSS, total CAGE signal and additional information for all TCs from specified CAGE dataset (sample). If `returnInterquantileWidth = TRUE`, interquantile width for each TC is also calculated using provided quantile positions.

### Author(s)

Vanja Haberle

Charles Plessy

### See Also

Other CAGEr accessor methods: `CTSSclusteringMethod()`, `CTSScoordinatesGR()`, `CTSScumulativesTagClusters()`, `CTSSnormalizedTpmDF()`, `CTSStagCountDF()`, `GeneExpDESeq2()`, `GeneExpSE()`, `consensusClustersGR()`, `expressionClasses()`, `genomeName()`, `inputFilesType()`, `inputFiles()`, `librarySizes()`, `sampleLabels()`, `seqNameTotalsSE()`

Other CAGEr clusters functions: `CTSSclusteringMethod()`, `CTSScumulativesTagClusters()`, `CustomConsensusClusters()`, `aggregateTagClusters()`, `clusterCTSS()`, `consensusClustersDESeq2()`, `consensusClustersGR()`, `cumulativeCTSSdistribution()`, `plotInterquantileWidth()`, `quantilePositions()`

### Examples

    tagClustersGR( exampleCAGEexp, "Zf.high", TRUE, 0.1, 0.9 )
    tagClustersGR( exampleCAGEexp, 1
                 , returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9 )

[Package CAGEr version 2.0.2 Index]