testAnnotationBasedSpeciesSpecificNeofunctionalization: Statistically tests the NULL Hypotheses that the annotation...

In asishallab/GeneFamilies: Analyses different properties of gene families

Statistically tests the NULL Hypotheses that the annotation (function) based species specific Shannon Entropy found in the gene groups for 'spec.2.compare' is not greater than that of the other species. The population means are compared using a t.test and the whole distributions are compared using a Kolmogoroff Smirnoff test. Correction for multiple hypotheses testing is carried out using the 'BY' method (see base::p.adjust for more details).

Description

Statistically tests the NULL Hypotheses that the annotation (function) based species specific Shannon Entropy found in the gene groups for 'spec.2.compare' is not greater than that of the other species. The population means are compared using a t.test and the whole distributions are compared using a Kolmogoroff Smirnoff test. Correction for multiple hypotheses testing is carried out using the 'BY' method (see base::p.adjust for more details).

Usage

testAnnotationBasedSpeciesSpecificNeofunctionalization(entropy.df,
  spec.2.compare, other.specs)

Arguments

entropy.df	The result of calling function computeSpeciesSpecificAnnotationDiversityPerGroup(...)
spec.2.compare	The species which to compare to all others.
other.specs	The species to compare pairwisely with spec.2.compare

Value

An instance of base::data.frame with 4 columns. The first two indicate which two species are compared in the respective row, the 3rd column holds the P-Values obtained from the pairwise T-Test, and the 4th column the P-Value obtained from the KS-Test. All P-Values are corrected for multiple hypotheses testing.

asishallab/GeneFamilies documentation built on July 28, 2024, 11:44 a.m.