MRCATestclass {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
: onesided pvalue 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.