probOfNSitesByChance: Calculate probability of N chance 'convergent' sites

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

Description

Calculate the probability that n sites between the two species will satisfy the conditions of convergent evolution by chance.

Usage

probOfNSitesByChance(
  tree,
  phydat,
  spe1,
  spe2,
  m,
  n,
  p = (1/20),
  t = NA,
  type = c("abs", "score")
)

Arguments

tree	A phylogenetic tree
phydat	PhyDat object containing corresponding alignment information
spe1	The name of species 1
spe2	The name of species 2
m	The length of the genes. (Must of equal length)
n	The number of potential convergent sites
p	The fraction of the amino acid at the target position in the evaluated genome. (Default is 1/20)
t	threshold for score option
type	Type of analysis: 'abs' for basic model or 'score' for by convergence score model

Value

Scaled likelihood that the amino acids satisfying the conditions of convergent evolution is by chance.

Examples

## Not run: 
probOfNSitesByChance(tree, "Human", "Chimp", 20, 2)

## End(Not run)

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