R: S4 class defining edge significance

MRCATest-class {alakazam} | R Documentation

## S4 class defining edge significance

### Description

`MRCATest` defines the significance of enrichment for annotations appearing at the MRCA of the tree.

### Usage

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

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

### Arguments

`x` | MRCATest object.
`y` | ignored.
`...` | arguments to pass to plotMRCATest.

### Slots

`tests`

  data.frame describing the significance test results with columns:

  - `ANNOTATION`: annotation value.

  - `COUNT`: observed count of MRCA positions with the given annotation.

  - `EXPECTED`: expected mean count of MRCA occurance for the annotation.

  - `PVALUE`: one-sided p-value for the hypothesis that the observed annotation abundance is greater than expected.

`permutations`

  data.frame containing the raw permutation test data with columns:

  - `ANNOTATION`: annotation value.

  - `COUNT`: count of MRCA positions with the given annotation.

  - `ITER`: numerical index define which permutation realization each observation corresponds to.

`nperm`

  number of permutation realizations.

[Package alakazam version 0.3.0 Index]