stanstrup / peakabro Goto Github PK

Would be nice if you could define a simple common use case, i.e. define a list of compounds that you would like to annotate and provide the code how this could/can be done.

This would also showcase your tidyverse approach, so I could check if an S4 approach could be implemented (in parallel?).

@stanstrup, I was wondering where you plan to distribute/add the package? Do you want to add it to CRAN or Bioconductor (I would not host exclusively on github)?.
I personally would prefer Bioconductor, because of the regular release cycles, possibility to add annotation data and because other related packages are already in Bioc (e.g. xcms ChemmineR).

I would like to see PeakABro added to Bioconductor, with the package not containing compound data, but only the code to generate and use these. The compound data (being versioned!) could ideally be added to AnnotationHub.

Note that if it's going to be Bioconductor it has to fulfill some criteria (http://www.bioconductor.org/developers/package-guidelines/) and also conform (more or less) their coding style (http://bioconductor.org/developers/how-to/coding-style/ - specifically, make sure that the lines in the R sources, including comments and documentations, are not longer than 80 character).

shinyBS is not maintained and buggy.

Note when a compound have been annotated to several features.
Useful to know if a compound have been annotated to other features too.

1. Which databases can I include data from?
2. If there are ones I cannot they will need to be download and table generated by the user. Is there such a thing as "in-package cache"?
3. Which license can the package have if it includes db data?
4. Is license a concern at all? As far as I know data cannot be copyrighted so is there any concern at all?

• MONA (lipidblast) is CC BY 4.0. So should be OK? http://mona.fiehnlab.ucdavis.edu/documentation/license
• I cannot find what license lipidmaps have.
• Seems hmdb require explicit permission to include http://www.hmdb.ca/downloads

The info I extract is: id, name, inchi, formula, and mass..

For the moment I force-removed the files until this is settled.

Names and structures don't match:
https://bitbucket.org/fiehnlab/mona/issues/200/lipidblast-mismatch-between-name-and

Functions added to package:

• LipidMaps
• LipidBlast
• HMDB
• MyCompoundDB
• PhenolExplorer
• PubChem. Too big? Not really useful?

License situation clearified

• LipidMaps
• LipidBlast - Confirmed CC BY. So OK with attribution.
• HMDB
• MyCompoundDB
• PhenolExplorer
• PubChem. Too big? Not really useful?

Please suggest.

Not sure why this is.
The first nest should be defined here:
https://github.com/stanstrup/PeakABro/blob/master/R/peaklist_browser.R#L248

But something is very off. It seems suddenly to be counting backwards.

Second nesting defined here:
https://github.com/stanstrup/PeakABro/blob/master/R/peaklist_browser.R#L110

move load.camera.rules and adduct lists to https://github.com/stanstrup/common_mz.
To avoid loading the heavy chemhelper.
Also option to not warn about conflicts.

@stanstrup, very nice work indeed! Always wanted to have such a packages and also started implementing something (https://github.com/jotsetung/xcmsExtensions), but never too serious.

My suggestion(s):

Keep functionality separate from the data:
Have dedicated data packages. This allows to have data packages from different sources or from different versions. See e.g. ensembldb and the EnsDb.Hsapiens.v75 package, or GenomicFeatures and the separate TxDb packages.

Define a CompoundDb class with main methods to query and access the database. E.g. have a method compound that retrieves compounds from the database and supports multiple filters. I know that's a little different setup (Bioconductor's rich, S4-based) than the tidyverse one, still, I think one could combine both worlds.

One could then define e.g. a HMDB class that simply extends the CompoundDb to accommodate HMDB-specific fields and attributes.

What might also be interesting is to implement the filters (or create filters that extend) AnnotationFilter (e.g. MzFilter or MassFilter). The MzFilter would have to calculate the mass for the provided mz. Ideal would be to have a MassFilter that takes a MzFilter as input, calculated the theoretical mass for the mz and returns a MassFilter.

The big advantages of having this setup would be:

• Versioned data packages.
• Data packages could be added to AnnotationHub.
• Using the same interface (methods and filters) for different data resources
  simplifies the use for the user (e.g. use the same method to retrieve
• Integration into Bioconductor. Common concept for annotation resources.
• You don't have to worry about licensing of the data resource in the main
  package. Each data package could/should have its own version. For those that
  don't allow sharing the data you could just provide the functionality to
  create the resource in the package and let it to the user to create the
  package for themselfs (if they have the license to do so).

I would be happy to contribute here (especially related to the database class,
interface methods and filters as I did all this already in ensembldb).

open for discussion

The browser could link to the resource page for each compound.

Either in the annotation or in the compounddbs allow expansion of possible biological adducts. We can use the list from mycompoundID:
http://www.mycompoundid.org/mycompoundid_IsoMS/reaction.jsp

If the same View button is clicked twice it doesn't react since the value doesn't change.
I have asked in many places that use the same code for a solution. So far nothing.

The relevant part is here: https://github.com/stanstrup/PeakABro/blob/master/R/peaklist_browser.R#L165

https://stackoverflow.com/questions/38575655/shiny-modules-namespace-outside-of-ui-for-javascript-links
https://stackoverflow.com/questions/45739303/r-shiny-handle-action-buttons-in-data-table
https://stackoverflow.com/questions/40107022/r-shinybs-popup-window
https://stackoverflow.com/questions/46593607/datatable-with-nesting-child-rows-and-modal