get_meanMeth_islands: Compute the Mean Methylation of CpG Islands

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

Compute the Mean Methylation of CpG Islands

Description

This function calculates the mean methylation level for CpG islands across all tree tips.

Usage

get_meanMeth_islands(index_islands, data)

Arguments

index_islands	A numeric vector specifying the indices of genomic structures corresponding to islands.
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 tip has the same number of structures, and each structure has the same number of sites across tips.

Value

A list where each element corresponds to a tree tip and contains a numeric vector representing the mean methylation levels for the indexed CpG islands.

Examples

# Example data setup

data <- list(
  # Tip 1
  list(rep(1,10), rep(0,5), rep(1,8)),
  # Tip 2
  list(rep(1,10), rep(0.5,5), rep(0,8))
)

index_islands <- c(1,3)

get_meanMeth_islands(index_islands, data)

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