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.