MeanSiteFChange_cherry: Compute the Mean Site Frequency of Methylation Changes per...

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

Compute the Mean Site Frequency of Methylation Changes per Cherry

Description

This function calculates the weighted mean frequency of methylation changes at island and non-island genomic structures for each cherry in a phylogenetic tree. A cherry is a pair of leaf nodes (also called tips or terminal nodes) in a phylogenetic tree that share a direct common ancestor.

Usage

MeanSiteFChange_cherry(
  data,
  categorized_data = FALSE,
  tree,
  index_islands,
  index_nonislands
)

Arguments

data	A list containing methylation states at tree tips for each genomic structure (e.g., island/non-island). The data should be structured as data[[tip]][[structure]], where each structure has the same number of sites across tips. The input data must be prefiltered to ensure CpG sites are represented consistently across different tips. Each element contains the methylation states at the sites in a given tip and structure represented as 0, 0.5 or 1 (for unmethylated, partially-methylated and methylated). If methylation states are not represented as 0, 0.5, 1 they are categorized as 0 when value equal or under 0.2 0.5 when value between 0.2 and 0.8 and 1 when value over 0.8. For customized categorization thresholds use categorize_siteMethSt
categorized_data	Logical defaulted to FALSE. TRUE to skip redundant categorization when methylation states are represented as 0, 0.5, and 1.
tree	A phylogenetic tree in Newick format or a phylo object from the ape package. The function ensures the tree has a valid structure and at least two tips.
index_islands	A numeric vector specifying the indices of genomic structures corresponding to islands.
index_nonislands	A numeric vector specifying the indices of genomic structures corresponding to non-islands.

Details

The function first validates the tree and the input data structure. It then computes the per-cherry frequency of sites with different methylation states using get_siteFChange_cherry. The indices provided for islands and non-islands are checked for validity using validate_structureIndices. Finally, the function calculates the weighted mean site frequency of methylation changes for each cherry, separately for islands and non-islands.

Value

A data frame with one row per cherry, containing the following columns:

tip_names

A character string representing the names of the two tips in the cherry, concatenated with a hyphen.

tip_indices

A character string representing the indices of the two tips in the cherry, concatenated with a hyphen.

dist

A numeric value representing the sum of the branch distances between the cherry tips.

nonisland_meanFChange

A numeric value representing the weighted mean frequency of methylation changes in non-island structures.

island_meanFChange

A numeric value representing the weighted mean frequency of methylation changes in island structures.

Examples

# Example data setup
data <- list(
list(rep(1,10), rep(0,5), rep(1,8)), # Tip a
list(rep(1,10), rep(0.5,5), rep(0,8)), # Tip b
list(rep(1,10), rep(0.5,5), rep(0,8)), # Tip c
list(c(rep(0,5), rep(0.5, 5)), c(0, 0, 1, 1, 1), c(0.5, 1, rep(0, 6)))) # Tip d

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

index_islands <- c(1,3)
index_nonislands <- c(2)

MeanSiteFChange_cherry(data = data, 
                       categorized_data = TRUE, 
                       tree = tree, 
                       index_islands = index_islands,
                       index_nonislands = index_nonislands)

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