areCondSatisfied: areCondSatisfied

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

Description

Determine whether conditions are satisfied for two species to be convergently evolved at a given position.

Usage

areCondSatisfied(
  tree,
  phydat,
  spe1,
  spe2,
  pos,
  type = c("abs", "score"),
  threshold = NA,
  simMatrix = BLOSUM62
)

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
type	Type of analysis: 'abs' for basic model or 'score' for by convergence score model (AA position with ref to species 1; others are aligned to species 1)
threshold	score threshold above which a position is considered convergent
simMatrix	similarity matrix to quantify similarity between amino acids (default is BLOSUM62)

Value

TRUE if conditions are satisfied; FALSE if they are not.

Examples

## Not run: 
data(BLOSUM62)
areCondSatisfied(smallTree, primates, "Human", "Chimp", pos=1, type="abs", 1, BLOSUM62)
areCondSatisfied(tree, primates, "Human", "Chimp", pos=2, type="score", threshold=0, BLOSUM62)
areCondSatisfied(tree, primates, "Human", "Chimp", pos=3, type="score", threshold=0, BLOSUM62)

## End(Not run)

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