myoRDNA

A toolkit for analysing rDNA methylation data from muscle and used in unison with methylKit.

Installation

Given that this package is currently under development installation must performed using devtools. Please implement the following commands in the R terminal:

install.packages("devtools")

Once installation has completed

# Load devtools
library(devtools)

# Install the package from GitHub
install_github("MuscleOmicsLab/myoRDNA", branch = "main")

# Load the package
library(myoRDNA)

Functionality

absolute_rDNA_CN <- function(
    Meth_object,
    num_samples,
    autosomes = TRUE,
    rDNA_chr,
    diploid = TRUE)

This function calculates the absolute rDNA copy number for each sample in a Meth_object (e.g., a list of methylation data or coverage data).

relative_rDNA_CN <- function(
   Meth_object,
   num_samples,
   autosomes = TRUE,
   rDNA_chr,
   diploid = TRUE)

This function calculates the relative rDNA copy number for each sample in a Meth_object (e.g., a list of methylation data or coverage data).

get_unique_chr_names <- function(
   Meth_object,
   num_samples)

This function extracts the unique chromosome names from the first sample in a Meth_object (e.g., a list of methylation data) and checks if all samples have the same chromosomes.