convSiteData: Get number of convergent sites

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

Description

Get the number of potentially evolved convergent sites and print the probability that this occured by chance.

Usage

convSiteData(
  tree,
  phydat,
  spe1,
  spe2,
  t,
  type = c("abs", "score"),
  m = getm(tree, phydat, spe1, spe2)
)

Arguments

tree	A phylogenetic tree
phydat	An object of class phydat
spe1	The name of species 1
spe2	The name of species 2
t	threshold
type	Type of analysis: 'abs' for basic model or 'score' for by convergence score model
m	The length of each gene (Up to what is desired to be evaluated). Default is entire gene

Value

The number of potentially convergent sites

Examples

## Not run: 
convSiteData(smallTree, primates, "Human", "Chimp", 5)

## End(Not run)

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