Plan is to submit the CompoundDb package to Bioconductor. This would allow that we add later CompDb databases to BioC's AnnotationHub resource (such as e.g. CompDb from MassBank).
Things that have to be fixed before:
[ ] remove dependency on github repositories. Eventually remove the mass2mz and similar functions to calculate between exact mass and adducts/ion m/z. This code should go to RforMassSpectrometry/MetaboCoreUtils. @stanstrup, maybe also check if there is something from the commonMZ package that could go there?
[ ] clean up vignettes.
[ ] add a vignette/description how CompoundDb can be used for MassBank data.
Potential issues that will come up is:
inconsistency in function names (i.e. camelCase and snake_case - BioC, for historical reasons, prefers camelCase).
Plan is to submit the
CompoundDbpackage to Bioconductor. This would allow that we add laterCompDbdatabases to BioC'sAnnotationHubresource (such as e.g.CompDbfrom MassBank).Things that have to be fixed before:
mass2mzand similar functions to calculate between exact mass and adducts/ion m/z. This code should go toRforMassSpectrometry/MetaboCoreUtils. @stanstrup, maybe also check if there is something from thecommonMZpackage that could go there?CompoundDbcan be used for MassBank data.Potential issues that will come up is:
camelCaseandsnake_case- BioC, for historical reasons, preferscamelCase).