tagClusters {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 CAGEr object.

### Usage

    tagClusters(object, samples = NULL, returnInterquantileWidth = FALSE,
      qLow = NULL, qUp = NULL)

    ## S4 method for signature 'CAGEr'
    tagClusters(object, samples = NULL,
      returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL)

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

    ## S4 method for signature 'CAGEset'
    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, samples = NULL) <- value

    ## S4 replacement method for signature 'CAGEset,ANY,ANY'
    tagClustersGR(object, samples = NULL) <- value

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

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

### Arguments

`object` | A `CAGEr` object.
`samples` | 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` | Should the interquantile width for each tag cluster be returned.
`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.
`sample` | Label of one CAGE dataset (experiment, sample) for which to extract tag clusters. (For `tagClustersGR`, only one sample can be extracted.)
`value` | A `TagClusters` object.

### Value

Returns a `data.frame` 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 specified quantile positions and returned in the data frame.

### Author(s)

Vanja Haberle

### See Also

Other CAGEr accessor methods: `CTSSclusteringMethod`, `CTSScoordinates`, `CTSScumulativesTagClusters`, `CTSSnormalizedTpm`, `CTSStagCountTable`, `CTSStagCount`, `GeneExpDESeq2`, `GeneExpSE`, `genomeName`, `inputFilesType`, `inputFiles`, `librarySizes`, `sampleLabels`, `seqNameTotalsSE`

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

### Examples

    head(tagClusters( exampleCAGEset, "sample2"
                    , returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9))
    tagClustersGR(exampleCAGEexp, "Zf.high", TRUE, 0.1, 0.9)

[Package CAGEr version 1.22.3 Index]