methylbridgeR

A package for integrating diverse DNA methylation data from different platforms.

The goal of methylbridgeR is to provide a robust computational framework for integrating and harmonizing DNA methylation data from different technologies, such as Whole-Genome Bisulfite Sequencing (WGBS) and microarray platforms (e.g., Illumina 450k/EPIC). This package aims to solve the problem of mapping, normalizing, and bridging these datasets to enable consistent cross-platform comparisons and downstream analyses like deconvolution.

Project Status

This package is currently in active development. Core functionalities are being implemented to address the challenges of:

• Data ingestion
• Genomic coordinate standardization
• Intelligent mapping
• Quantitative normalization between platforms

Installation

You can install the development version of methylbridgeR from GitHub like so:

install.packages("devtools")
devtools::install_github("CogDisResLab/methylbridgeR")

Example

This is a basic example showing how to use a core functionality of methylbridgeR: mapping probes from an array reference to your higher-resolution WGBS data and generating a unified matrix for deconvolution.

First, load the package and some conceptual example data:

# Load the package
library(methylbridgeR)
library(dplyr)

# Conceptual WGBS dataset
wgbs_data <- tibble(
  chr = c("chr1", "chr1", "chr1"),
  start = c(100, 105, 115),
  end = c(101, 106, 116),
  cell1 = c(0.9, 0.8, 0.1),
  cell2 = c(0.85, 0.75, 0.15)
)

# Array probe annotation
array_annotation <- tibble(
  probe_id = "cg12345",
  chr = "chr1",
  start = 110,
  end = 111
)

# Map the array probe to WGBS data using a window-averaging strategy
mapped_data <- map_array_to_wgbs(
  wgbs_data = wgbs_data,
  array_annotation = array_annotation,
  mapping_strategy = "window_averaging",
  window_size = 20
)

# Print the mapped result
print(mapped_data)

# Generate a signature matrix (hypothetical function)
# signature_matrix <- generate_signature_matrix(mapped_data, cell_states = ...)

This will produce a table of methylation values from your WGBS data, summarized to match the locations of your array probes — essential for creating a signature matrix.