get_nonislandMeanFreqP: Calculate the Mean Frequency of Partially Methylated Sites in...

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

Calculate the Mean Frequency of Partially Methylated Sites in Non-Islands

Description

This function computes the mean frequency of partially methylated sites (with methylation state 0.5) for a set of genomic structures identified as non-islands.

Usage

get_nonislandMeanFreqP(
  index_nonislands,
  data,
  sample_n,
  categorized_data = FALSE
)

Arguments

index_nonislands	A vector containing the structural indices for non-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 partially methylated sites in the non-islands.

Examples

# Example usage:
index_nonislands <- 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_nonislandMeanFreqP(index_nonislands, data, sample_n, categorized_data = TRUE)

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