compute_fitch: Compute Fitch Parsimony for Methylation Categories

In MethEvolSIM: Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies

Compute Fitch Parsimony for Methylation Categories

Description

This function applies Fitch parsimony to determine the minimum number of changes required for methylation categories at tree tips.

Usage

compute_fitch(tree, meth, input_control = TRUE)

Arguments

tree	A rooted binary tree in Newick format (character string) or as an ape phylo object. Must have at least two tips.
meth	A matrix of methylation categories at the tree tips, with rows corresponding to tips (names matching tree tip labels) and columns corresponding to sites or structures.
input_control	Logical; if TRUE, validates input consistency.

Value

A list containing:

optStateSet

A list of sets of optimal states for the root at each site/structure.

minChange_number

A numeric vector indicating the minimum number of changes for each site.

Examples

tree <- "((a:1,b:1):2,(c:2,d:2):1.5);"

meth <- matrix(c("u", "m", "p", "u", "p", "m", "m", "u"), 
               nrow=4, byrow=TRUE, dimnames=list(c("a", "b", "c", "d")))
               
compute_fitch(tree, meth)

MethEvolSIM documentation built on April 12, 2025, 1:30 a.m.