R: S4 class defining a clonal abundance curve

AbundanceCurve-class {alakazam} | R Documentation

## S4 class defining a clonal abundance curve

### Description

`AbundanceCurve` defines clonal abundance values.

### Usage

    ## S4 method for signature 'AbundanceCurve'
    print(x)

    ## S4 method for signature 'AbundanceCurve,missing'
    plot(x, y, ...)

### Arguments

`x` | AbundanceCurve object
`y` | ignored.
`...` | arguments to pass to plotDiversityCurve.

### Slots

`abundance`

  data.frame with relative clonal abundance data and confidence intervals, containing the following columns:

  - `GROUP`: group identifier.

  - `CLONE`: clone identifier.

  - `P`: relative abundance of the clone.

  - `LOWER`: lower confidence inverval bound.

  - `UPPER`: upper confidence interval bound.

  - `RANK`: the rank of the clone abundance.

`bootstrap`

  data.frame of bootstrapped clonal distributions.

`clone_by`

  string specifying the name of the clone column.

`group_by`

  string specifying the name of the grouping column.

`groups`

  vector specifying the names of unique groups in group column.

`n`

  numeric vector indication the number of sequences sampled in each group.

`nboot`

  numeric specifying the number of bootstrap iterations to use.

`ci`

  confidence interval defining the upper and lower bounds (a value between 0 and 1).

[Package alakazam version 0.3.0 Index]