Expose the function to identify isotopes?

[jorainer]

Dear developers (@sneumann @Treutler) I wanted to ask if it would be possible to expose/export some CAMERA-internal core functionality as documented functions?

The reason for that: I think it would be helpful to be able to call some of the core functionality from CAMERA also from other packages or independently of CAMERA (and more importantly, the xcmsSet object). This would open up CAMERA also for other types of input data, e.g. if you just have a list of m/z and intensity values, find possible isotopes. And that is actually exactly my use case at the moment: I have a set of m/z values and related intensity values and would like to know which or if these could be isotopes from each other. So, is there a function in CAMERA that takes mz and intensity values and can predict isotopes on that? And if so, which is it and how can I call that?

[stanstrup]

Not tried it but seems you are looking for findIsotopesPspec in:

CAMERA/R/fct_findIsotopes.R

Line 27 in bc0e9fd

findIsotopesPspec <- function(isomatrix, mz, ipeak, int, params){

Some post-proccesing seems to be going on so perhaps there is not a single function that can be used direct:

CAMERA/R/xsAnnotate.R

Line 648 in bc0e9fd

isomatrix <- findIsotopesPspec(isomatrix, mz, ipeak, int, params)

[jorainer]

Thanks Jan! Yes I've also seen this function - but it's hard to understand what the individual parameters mean or are. But yes, I would like to have e.g. this function exported (and documented).

[sneumann]

Hi, I am open for PR and can (try) to help. But Carsten Kuhl is long gone from my group :-(

[jorainer]

I've just realized that there is a second way to find isotopes: findIsotopesWithValidation - which uses a completely different code basis to find isotopes. @sneumann is this one supposed to be the better approach that should be used by default now?