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.