compute_meanCor_i: Compute the Mean Correlation of Methylation State in Islands

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

Compute the Mean Correlation of Methylation State in Islands

Description

This function calculates the mean correlation of methylation states within island structures, allowing to exclude the shores.

Usage

compute_meanCor_i(
  index_islands,
  minN_CpG,
  shore_length,
  data,
  sample_n,
  categorized_data = FALSE
)

Arguments

index_islands	A vector containing the structural indices for islands.
minN_CpG	The minimum number of central CpGs required for computation.
shore_length	The number of CpGs at each side of an island to exclude (shores).
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 tips (samples) to process.
categorized_data	Logical defaulted to FALSE. TRUE to skip redundant categorization when methylation states are represented as 0, 0.5, and 1.

Details

The function processes only islands with a minimum length equal to 2 * shore_length + minN_CpG. If none has minimum length, returns NA

Value

A numeric value representing the mean correlation of methylation states in the central CpGs of islands.

Examples

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

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