probOfSiteConfig: probOfSiteConfig

In dinaIssakova/rgenesconverged: A Package for Estimating Probability of Convergent Evolution from Genomic Data

Description

Calculate the probability of the given configuration

Usage

probOfSiteConfig(tree, phydat, spe1, spe2, pos, p = (1/20), anc, x, y)

Arguments

tree	A phylogenetic tree
phydat	An object of class phydat.
spe1	The name of species 1
spe2	The name of species 2
pos	The position at which to evaluate if conditions are satisfied
p	The fraction of the amino acid at the target position in the evaluated genome. (Default is 1/20)
anc	ancestral AA value (for testing or internal input)
x	AA value of spe1 (for testing or internal input)
y	AA value of spe2 (for testing or internal input)

Value

Probability of given configuration

Examples

probOfSiteConfig(tree, primates, "Human", "Chimp", pos=1)

dinaIssakova/rgenesconverged documentation built on Jan. 7, 2020, 4:25 p.m.