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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Is it possible to find Antibiotic resistance Genes (ARGs) using Subset or other function? #599

Closed yasiromics closed 1 year ago

yasiromics commented 1 year ago

Hi! I have successfully loaded SQM data into R. thank you for all your help. I want to study the ARGs present in my metagenomic data. As the example data shows we can study different functions viz. carbohydrate, amino acid biosynthesis pathways, do we have any options for ARGs as well?

fpusan commented 1 year ago

Yes, but you need to know what term to search for (e.g. maybe "antibiotic resistance" will work as a search term, but maybe you need to refine and go for something like "beta-lactamase"). Alternatively, you can look for all the KOs in here (https://www.genome.jp/kegg/annotation/br01600.html) The way to search for several things at once is to use standard regexp syntax E.g. subsetFun(SQM, "K00001|K00002") will look for both terms at once.

yasiromics commented 1 year ago

Thanks for the prompt repones. I did try antibiotic resistance and individual KO Ids but to no avail. Can you kindly forward the link or the script to put all KO Ids into the above syntax at once?

fpusan commented 1 year ago

Not at the moment, sorry, but just copying all the KO ids into a text editor and replacing \n by | might do the trick.

yasiromics commented 1 year ago

Thank you. It worked

fpusan commented 1 year ago

Glad to hear! Closing issue