MRCATest-class {alakazam}R Documentation

S4 class defining edge significance

Description

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

Usage

## S4 method for signature 'MRCATest'
print(x)

## S4 method for signature 'MRCATest,missing'
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.


[Package alakazam version 1.1.0 Index]