README.md

In netome/m2path: m2path

m2path

m2path is a tool for omics pathway enrichment analysis

• Citation: if you use the m2path software, please cite our manuscript: Rahnavard et al. m2path: a generic tool for omics enrichment analysis.
• This page provides a quick toturial (workshop orinted) infomration to start and use m2path.
• An extnsive User Manual is provides in wiki which contains explanation for all options.

Setup m2path

• Setp 1: install m2path and its depedencies
• Setp 2: download refrence mapping databases

What are the steups unique to your OS? What did you need to skip in your installation steps? Did you need any package that is not listed in the requirements?

Input files format

The input file can be generated by massPattern package.

m2path demo

| | logFC | statistic | P.Value ----------------|----------------|-------------|------------- HMDB00696 | -0.066838102 | 60 | 0.513722581 HMDB00191 | -0.167002899 | 68 | 0.84283599 HMDB00148 | -0.106438214 | 60 | 0.513722581 HMDB00168 | -0.029952907 | 69 | 0.887385935 HMDB00641 | -0.040854959 | 64 | 0.670659533 HMDB00177 | -0.050286514 | 55 | 0.347357919 HMDB00517 | -0.0184334 | 70 | 0.932300503 HMDB00182 | -0.001386226 | 70 | 0.932300503 HMDB00883 | 0.04519753 | 74 | 0.932300503 HMDB00687 | 0.049785325 | 73 | 0.977402191 HMDB00172 | 0.04173989 | 74 | 0.932300503 HMDB00159 | -0.034784137 | 72 | 1 HMDB00158 | 0.034486909 | 76 | 0.84283599 HMDB00929 | 0.071698012 | 80 | 0.670659533 HMDB00162 | -0.030734138 | 67 | 0.798745339 HMDB00725 | 0.070803166 | 92 | 0.265669584

and continues ...

Run

# load the library
library(m2path)

# smpdb_metabolites_db has the path to the file for SMPDB metabolites database
# call the function
res <- m2path::m2path(score_set='/path-to-input/stats_table.txt',
output='/path-to-output/', 
mapper_pathway2hmdb_file= smpdb_metabolites_db, # or '/path-to-data/smpdb_metabolites.csv', 
mapper_oldhmdb_newhmdb_file= '/path-to-data/ParsedHMDB_v4.0.csv')

Output files

pathway | pval | fdr | n | set_enrichment_score ---------------------------------|---------------|---------------|------|---------------------- Arginine and Proline Metabolism | 0.333333333 | 0.333333333 | 10 | 0.425686617 Histidine Metabolism | 0.179104478 | 0.268656716 | 10 | 0.502342185 Purine Metabolism | 0.001369986 | 0.004109959 | 10 | 0.701651617

netome/m2path documentation built on Dec. 3, 2019, 11:02 p.m.