Comments (2)
yes, you can also create a database completely from skratch with a single data.frame
(or tibble
) - you can find a description of the required columns in the help of the createCompDb function.
And yes, it should be possible to add MS2 spectra from a Spectra
object - see help of the insertSpectra function. Let me know if something is not working with this one. Importing data from Msp files into a Spectra
should also work pretty well now with the MsBackendMsp package.
For the adduct nomenclature - for your database you can use whatever you prefer. Maybe also have a look at MetaboCoreUtils::adductNames()
to see what we have available and use that nomenclature for those overlapping.
Regarding isotopically labelled compounds, I guess you could add them to the compound
table providing their specific exact mass? Note that you can also add any additional columns to that table when you create the CompDb
database. The ones listed in the documentation above are mandatory, but you can add as many additional ones as you like (and the mandatory ones can also contain missing values).
As always, please let me know if you run into any problems or if something is not working as expected and I will adapt. It's hard to foresee all possible use cases, but the system should be flexible enough so that we can adapt it.
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I've just updated the package with PR #97 . Creating custom CompDb
databases should now be a little easier. I've also added a new section to the respective vignette.
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Related Issues (20)
- Create an IonDb with all theoretical adducts for a CompoundDb
- Function to combine/concatenate CompDb databases
- Add an insertCompound function HOT 1
- Availability of functions to create empty CompDB and insert and delete compounds HOT 2
- Seeking suggestions for database development (HMDB version 5) HOT 2
- Pass skipErrors to read.SDFset through compound_tbl_sdf? HOT 4
- Replace mass2mz and mz2mass with the ones from MetaboCoreUtils
- Rename table "compound" into "ms_compound"
- Implement a StandardsDb that extends CompoundDb HOT 11
- Update the MsBackendCompDb HOT 1
- insertIon method HOT 4
- non integer msLevel values HOT 3
- Add possibility to delete (inserted or existing) ions or MS/MS spectra
- Prepare for Bioconductor submission HOT 3
- Arbitrary columns in insertIon
- Transfer of CompoundDb
- Support import from MoNa MSP files HOT 1
- Issue with GitHub install of CompoundDb HOT 3
- mass2mz method for CompDb HOT 6
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