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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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What does --depth in enricm explore mean? #95

Open TYMichaelsen opened 4 years ago

TYMichaelsen commented 4 years ago

Hi Joel, This is related to #17 (your'e probably busy now!) but could I get just brief elaboration on the --depth parameter in enrichm explore besides whats available from the -h: "Number of steps to take into the metabolic network"

geronimp commented 4 years ago

Hey,

No worries - when constructing a network with explore, it takes "steps" into metabolism from a set of compounds you specify. The depth is the number of "steps" that are taken when creating a network. A "step" is when enrichm takes a compound (beginning with the original compounds specified to enrichm explore) and identifies all the reactions (and their end-products) that utilise it. In the next step, the same is done for the compounds were are produced from the previous compound, and so on. In that way you can make a localised network for specific compounds to explore how they're metabolised, rather than looking at the whole network, which tends to be a hairball. Does that make sense? Please let me know if there is anything else that isnt clear.

TYMichaelsen commented 4 years ago

Thanks for the quick response!

That makes sense - and the numbers reported for each MAG in network.tsv denotes present/absent in the given MAG? Besides 0 and 1 I am also getting decimal numbers (0.333, 1.677 etc.), what does that mean? I have not provided any abundance matrix to the program.