tagClustersQuantile {CAGEr} | R Documentation

## Quantile metadata stored in CAGEr objects.

### Description

Accessor functions to quantile metadata.

### Usage

    tagClustersQuantile(object, samples = NULL, q = NULL)

    ## S4 method for signature 'TagClusters'
    tagClustersQuantile(object, samples = NULL,
      q = NULL)

    ## S4 method for signature 'CAGEexp'
    tagClustersQuantile(object, samples = NULL,
      q = NULL)

    tagClustersQuantileLow(object, samples = NULL, q = NULL)

    ## S4 method for signature 'CAGEset'
    tagClustersQuantileLow(object, samples = NULL,
      q = NULL)

    ## S4 method for signature 'CAGEexp'
    tagClustersQuantileLow(object, samples = NULL,
      q = NULL)

    tagClustersQuantileUp(object, samples = NULL, q = NULL)

    ## S4 method for signature 'CAGEset'
    tagClustersQuantileUp(object, samples = NULL,
      q = NULL)

    ## S4 method for signature 'CAGEexp'
    tagClustersQuantileUp(object, samples = NULL,
      q = NULL)

    tagClustersQuantileLow(object, samples = NULL) <- value

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

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

    tagClustersQuantileUp(object, samples = NULL) <- value

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

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

### Arguments

`object` | A `CAGEr` object.
`samples` | Sample name(s), number(s) or `NULL` (default) for all samples.
`q` | A single quantile (not a list)
`value` | A list (one entry per sample) of data frames with multiple columns: `cluster` for the cluster ID, and then `q_0.n` where `0.n` indicates a quantile.

### Value

Returns a `data.frame` where the first column gives cluster names and the next columns give quantile positions, in zero-based chromosome coordinates (because the tag clusters in CAGEset objects are represented in zero-based coordinates as well)).

[Package CAGEr version 1.30.3 Index]