MethScope-MRMP

Generate an MRMP reference

MethScope includes pre-defined MRMP references, and you can also build your own from a methylation atlas.

Prerequisites

1. Install YAME for .cg processing: https://zhou-lab.github.io/YAME/
2. Prepare a reference methylation .cg file (for example, an atlas or merged reference panel)
3. Install and load MethScope

library(MethScope)

Step 1: Binarize the reference .cg file

Convert methylation proportions into binary strings. The default threshold is 0.5; adjust with -b if needed.

yame rowop example.cg -o binstring > example_binstring

Step 2: Build MRMP pattern definitions

Use GenerateReference() to identify recurrent patterns.
min_CG controls the minimum CpGs per MRMP (default: 50).

GenerateReference(binary_file = "example_binstring", min_CG = 50)

This step generates a patterns.txt file.

Step 3: Pack patterns into a .cm reference

Pack patterns.txt into a .cm file that can be passed as reference_pattern in GenerateInput().

yame pack -f s patterns.txt patterns.cm

Build MRMP references from cell-type pseudobulks

If cell-type labels are available, pseudobulked profiles can produce robust cell-type-informed MRMP references.

Step 1: Create pseudobulk profiles per cell type

Prepare a text file (samples.txt) containing sample IDs for one cell type, then aggregate with musum.

yame subset -l samples.txt example.cg | yame rowop -o musum - example_pseudobulk.cg

Step 2: Repeat per cell type and build MRMPs

Run the same workflow above (binstring -> GenerateReference -> yame pack) on each pseudobulk or combined pseudobulk panel.

For running a full parallelized multi-cell-type script, please refer to: https://github.com/zhou-lab/MethScope/blob/main/analysis/GenerateReference.sh

After generating patterns.cm, use it as the custom MRMP reference in downstream MethScope analyses.