MRCATest-class - S4 class defining edge significance

Description

MRCATest defines the significance of enrichment for annotations appearing at the MRCA of the tree.

Usage

"print"(x)
"plot"(x, y, ...)

Arguments

x
MRCATest object.
y
ignored.
arguments to pass to plotMRCATest.

Slots

tests
data.frame describing the significance test results with columns:
  • ANNOTATION: annotation value.
  • COUNT: observed count of MRCA positions with the given annotation.
  • EXPECTED: expected mean count of MRCA occurance for the annotation.
  • PVALUE: one-sided p-value for the hypothesis that the observed annotation abundance is greater than expected.
permutations
data.frame containing the raw permutation test data with columns:
  • ANNOTATION: annotation value.
  • COUNT: count of MRCA positions with the given annotation.
  • ITER: numerical index define which permutation realization each observation corresponds to.
nperm
number of permutation realizations.