combineSpectra not working for readMSData MSNexp

[joannawolthuis]

Hi there! I'm trying to import DI-MS data and sum/combine the positive and negative mode spectra scans, but get the following (same for in memory):. The documentation notes that an MSnExp should be a possible input, but it isn't working for me...

files = c("~/Downloads/rawdata/file.mzML", "~/Downloads/rawdata/file2.mzML")
mem <- readMSData(files, mode = "onDisk", msLevel. = 1)
combineSpectra(mem)
# Error in (function (classes, fdef, mtable)  : 
#   unable to find an inherited method for function ‘combineSpectra’ for signature ‘"OnDiskMSnExp"’

[sgibb]

Indeed in contrast to the manual page

MSnbase/man/combineSpectra.Rd

Line 13 in 9e2d703

\item{object}{A \linkS4class{MSnExp} or \linkS4class{Spectra}}

combineSpectra isn't define for neither MSnExp nor OnDiskMSnExp objects.

@jorainer is this intended or a bug?

[jorainer]

Hm - seems I implemented that only for Spectra and forgot about the MSnExp implementation...

@joannawolthuis , could you first please check if the Spectra implementation would work for you?

To get a Spectra object you would have to call:

sps <- Spectra(spectra(mem))

on your mem object above.

[jorainer]

I've implemented the combineSpectra,MSnExp method and made a pull request (#475). With that it will be possible to call combineSpectra on MSnExp and OnDiskMSnExp objects - the result will be a MSnExp object.

[joannawolthuis]

Hi :-) Thanks so much for taking a look so quickly! I was going to try with the Spectra implementation but it seemed a bit hacky to get it back into the MSnexp format for further peak calling, so I'll wait for this pull to go through :-)

[jorainer]

Closing this issue. Feel free to reopen if needed.