familyExpanded: Alternative method to detect expanded or compressed families...

In asishallab/GeneFamilies: Analyses different properties of gene families

Alternative method to detect expanded or compressed families comparing one species with the background of the others. P-Values are obtained from an outlier chisquare test; see package outliers::chisq.out.test(...) for details.

Description

Alternative method to detect expanded or compressed families comparing one species with the background of the others. P-Values are obtained from an outlier chisquare test; see package outliers::chisq.out.test(...) for details.

Usage

familyExpanded(x, test.species = "chi",
  background.species = setdiff(names(x), test.species),
  expansion.test = max)

Arguments

x	named integer vector representing the gene family to test. x holds the number of gene members per species.
test.species	a string being used ase a name in argument 'x' indicating which species is the alternative hypothesis of expansion (or contraction) based upon
background.species	a character vector holding the names of the species the background distribution of numbers of the species specific family members is based upon.
expansion.test	boolean indicating whether to test for expansion (default TRUE) or compression (set to FALSE).

Value

numeric p-value obtained from outliers::chisq.out.test(x) or NA, if expansion-test does not indicate a candidate outlier.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.