get_islandMeanFreqM: Calculate the Mean Frequency of Methylated Sites in Islands

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

Calculate the Mean Frequency of Methylated Sites in Islands

Description

This function computes the mean frequency of methylated sites (with methylation state 1) for a set of structures identified as islands.

Usage

get_islandMeanFreqM(index_islands, data, sample_n, categorized_data = FALSE)

Arguments

index_islands	A vector containing the structural indices for islands.
data	A list containing methylation states at tree tips for each genomic structure (island / non-island) For a single tip: data[[structure]]. For multiple tips: data[[tip]][[structure]]. 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
sample_n	The number of samples (tips) to process.
categorized_data	Logical defaulted to FALSE. TRUE to skip redundant categorization when methylation states are represented as 0, 0.5, and 1.

Value

A numeric value representing the mean frequency of methylated sites in the islands.

Examples

# Example usage:
index_islands <- c(1, 3)
data <- list(
  list(c(0.5, 1, 0.5), c(0, 0.5, 1), c(1, 0, 0.5)), # tip 1
  list(c(0.5, 0.5, 0), c(1, 0.5, 0.5), c(0.5, 0.5, 1)) # tip 2
)
sample_n <- 2
get_islandMeanFreqM(index_islands, data, sample_n, categorized_data = TRUE)

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