mass2mz method for CompDb about compounddb HOT 6 OPEN

What you observed/described above is the default behaviour of the compounds function: it uses by default distinct in the SQL call, thus returning only unique results. To ensure all formulas are returned (even duplicated ones) I would suggest to use compounds(cmp_db, c("compound_id", "exactmass")).

from compounddb.

@RogerGinBer are you currently working on this? That would be totally fine for me - contribution in form of a PR (pull request) highly welcome

from compounddb.

Yes, I'm working on it 👍
I believe we should also have a mass2mz method (or perhaps a different function, like formula2mz), that, given a list of formulas and adducts, calculates each formula's neutral mass and then calls mass2mz to generate a formula-adduct mz matrix.
This way, the CompDb method just has to extract the formulas from the object and call formula2mz. Would that make sense?

from compounddb.

The CompDb provides already masses (monoisotopic), so it would be a little computational overhead to first calculate the masses from the chemical formulas. So I would maybe start with a mass2mz first.

Actually, a formula2mz might be a nice addition for MetaboCoreUtils - it could simply combine the MetaboCoreUtils::calculateMass function (that can also calculate masses from e.g. "[13C3]C3H12O6") and then calculate m/z using the MetaboCoreUtils::mass2mz. If interested you could do a PR with that function in MetaboCoreUtils?

from compounddb.

Sure thing! I read in the create-compounddb vignette that the exact_mass column could have NA values, so that's why I thought of doing it from the formula. But yes, makes more sense to use the mass directly, when available

Yes, I'll open an issue at MetaboCoreUtils and start a PR on that

from compounddb.

Also, I've found some unexpected behavior with the compounds accessor using the HMDB example CompDb:
compounds(cmp_db, "exactmass") gives only 8 results (removes one duplicate 104.0473), while compounds(cmp_db)$exactmass returns them all 9.

Is this how it's supposed to work?

from compounddb.