Code Monkey home page Code Monkey logo

Comments (2)

jorainer avatar jorainer commented on July 18, 2024

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.

from compounddb.

jorainer avatar jorainer commented on July 18, 2024

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.

from compounddb.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.