EdgeTest-class - S4 class defining edge significance

Description

EdgeTest defines the significance of parent-child annotation enrichment.

Usage

"print"(x)

"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.