MRCATest-class {alakazam} | R Documentation |
MRCATest
defines the significance of enrichment for annotations appearing at
the MRCA of the tree.
## S4 method for signature 'MRCATest' print(x) ## S4 method for signature 'MRCATest,missing' plot(x, y, ...)
x |
MRCATest object. |
y |
ignored. |
... |
arguments to pass to plotMRCATest. |
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.