EdgeTest-class: S4 class defining edge significance

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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.

alakazam documentation built on Nov. 5, 2025, 6:55 p.m.