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 1.1.0 Index]