Generate MRMP reference
We provided three reference MRMPs definitions, and if you want to
create your own MRMPs definitions, please follow the following
tutorial.
- Download and install YAME (https://zhou-lab.github.io/YAME/)
- Process you methylation reference file into .cg file
- run the following yame rowop code to binarize your input file
(default threshold is at 0.5, use -b to adjust threshold if needed)
yame rowop example.cg -o binstring > example_binstring
- Generate the reference definition (default min CG per MRMP is 50,
adjust the threshold if needed with min_CG)
GenerateReference(example_binstring)
- Pack the generated pattern.txt into .cm file which can be directly
used as reference_pattern in our GenerateInput function.
yame pack -f s patterns.txt patterns.cm
Generate MRMPs reference from cell type pseudobulks
It might be useful to generate the MRMPs reference from cell type
pseudobulks if the cell type label is available.
- Obtain a txt file that contains sample names belong to oen cell type
that you want to merge together from the cell type label.
- Generate the pseudobulk profile using yame subset and rowop
yame subset -l samples.txt example.cg | yame rowop -o musum - example_pseudobulk.cg
Please check our full code GenerateReference.sh in our analysis
folder (https://github.com/zhou-lab/MethScope) as a reference
for in parallel process multiple cell types. After obtaining the
pseudobulk profile, it will be the same steps as above to obtain the
MRMPs definition file.