I am interested in using MetaboAnalystR to run mummichog on a set of files where I have already done the pre-processing. I have been able to setup MetaboAnalystR in R and run all the analysis steps I want. In reading through the PDF with the different modules, each PDF ends with a description of the PDF that is generated as a Sweave report. The report is helpful, but does not seem to generate the csv file that I am looking for (mummichog_matched_compound_all.csv). I poked around in GitHub, and note that the recommendation is to get this file from the set of files that can be downloaded from the website. While I can see how to do that, I would like this to self-contained in R. Are you willing the share the R script that is generating this file (and the mummichog_pathway_enrichment.csv file, though I found most of that by using: mummitable ← mSet$mummi.resmat)?
Thanks.
Krista Longnecker
My apologies, I just realized that when I run PerformPSEA, MetaboAnalystR saves these data files in the working directory. I was expecting to be able to setup an output directory and did not think to look in the most obvious place.