Writing/exporting raw data objects

[lgatto]

This discusses naming the function in PR #257, also discussed here. Current suggestions are

1. write - Jo's first choice
2. writeMSData as a generic with methods in mzR and MSnbase
3. export - suggested on bioc-devel

Please share you opinions/votes below.

[lgatto]

Given the feedback on bioc-devel, I suggest we drop write.

From a user's perspective, I think writeMSData fits well with readMSData. Also, the equivalent of export, would be import, which we don't use. I think having writeMSData in mzR makes me want this option even more, as we would keep the naming consistent across packages.

So my vote would go for 2.

Quick question - what would be the difference in writing an MSnExp object and an mzRpwiz object?

[jorainer]

Jup, let's drop write. I tend to 3 (export) - for 2 we have to make writeMSData a generic with arguments becoming potentially tricky:

• writeMSData in mzR needs: files (character), header (data.frame) and data (list).
• writeMSData in MSnbase does not have a header. We would need to make the generic as writeMSData signature(data = "MSnExp", file = "character")... thinking it over its doable. So OK for me to go for that.

[lgatto]

We could have

setGeneric("writeMSData", function(object, file, ...) standardGeneric("writeMSData"))

and then in mzR

setMethod("writeMSData", 
           c("list", ## list of spectra
             "character", ## file name 
             "data.frame", ## header 
             ...) 
   function(object, filenames, header) { ... })

and in MSnbase

setMethod("writeMSData", 
           c("MSnExp", ## list of spectra
             "character", ## file name 
             ...) { 
  function(object, files) {
    header <- fData(object)
     ...
})

By the way, I would prefer filename rather than filenames, given #257.

[jorainer]

OK, let's go for that - do you add the generic to ProtGenerics @lgatto ?

[jorainer]

Made a pull request in ProtGenerics: rformassspectrometry/ProtGenerics#5

[lgatto]

Merged. Will push to bioc asap (but I'm at a meeting whole day).

[lgatto]

Done