R: S4 class defining edge significance

EdgeTest-class {alakazam} | R Documentation

## S4 class defining edge significance

### Description

`EdgeTest` defines the significance of parent-child annotation enrichment.

### Usage

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

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

### Arguments

`x` | EdgeTest object.
`y` | ignored.
`...` | arguments to pass to plotEdgeTest.

### Slots

`tests`

  data.frame describing the significance test results with columns:

  - `PARENT`: parent node annotation.

  - `CHILD`: child node annotation

  - `COUNT`: count of observed edges with the given parent-child annotation set.

  - `EXPECTED`: mean count of expected edges for the given parent-child relationship.

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

`permutations`

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

  - `PARENT`: parent node annotation.

  - `CHILD`: child node annotation

  - `COUNT`: count of edges with the given parent-child annotation set.

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

`nperm`

  number of permutation realizations.

[Package alakazam version 0.3.0 Index]