implement `MsBackendRawDiag.R` for `Spectra`

[cpanse]

https://github.com/fgcz/rawDiag/blob/0d3f5d465296240d2c100357c95a2777d7e74770/R/rawDiag.R#L496

https://github.com/rformassspectrometry/Spectra

[tobiasko]

I think this task is not named correctly. If we go for this we do not want to have a coercion function, but we need to def. a backend that can access spectral data stored in raw files:

https://github.com/rformassspectrometry/Spectra/blob/master/man/MsBackend.Rd

The easiest might be to create an MsBackendDataFrame that keeps all data in memory. A backend that keeps peak lists on disk might be a cool thing. Here lazy evaluation could become pretty powerful. One could also think about mixed models. Have metadata in memory and keep spectral data on disk.

[lgatto]

Yes, I confirm that the correct way forward would be to define a backend that uses the mono libraries to access the raw data and the metadata in a DataFrame - see the MsBackendMzR for that does exactly that but with mzR.

[cpanse]

@lgatto @tobiasko yep; I am not so fast ... upgrading BioC form 3.7 to devel on my playground box reminds me of my 1st SuSE4.2 install in 1996. (except changing the install disk 1-3)

[tobiasko]

@lgatto, would you suggest to bundle the code for the alternative backend into a separate bioconductor package? Will bioconductor be ok with hosting Thermo DLLs?

https://planetorbitrap.com/rawfilereader

[lgatto]

Yes, a separate MsBackendRawDiagpackage on github that ships the DLLs is an option. Or, a function that downloads them upon first initialisation is also a solution.

[lgatto]

Pinging @jorainer

[cpanse]

1. All in memory

library(rawDiag)
(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))
system.time(PLS <-readScans(rawfile))
system.time(DF <- as.peaklistSet.DataFrame(PLS))
DF$fromFile = as.integer(1)

if(require(Spectra)){
  rawDiagSample <- MsBackendDataFrame()
  system.time(BE <- backendInitialize(object=rawDiagSample, files=rawfile, spectraData=DF))
}

R> library(rawDiag)
R> (rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))
[1] "/home/cp/R/x86_64-pc-linux-gnu-library/3.6/rawDiag/extdata/sample.raw"
R> system.time(PLS <-readScans(rawfile))
   user  system elapsed 
  0.123   0.053   0.643 
R> system.time(DF <- as.peaklistSet.DataFrame(PLS))
   user  system elapsed 
  0.029   0.000   0.029 
R> DF$fromFile = as.integer(1)
R> 
R> if(require(Spectra)){
+    rawDiagSample <- MsBackendDataFrame()
+    system.time(BE <- backendInitialize(object=rawDiagSample, files=rawfile, spectraData=DF))
+  }
   user  system elapsed 
  0.122   0.000   0.122 
R> BE
MsBackendDataFrame with 574 spectra
      msLevel     rtime scanIndex
    <integer> <numeric> <integer>
1           1     0.097         1
2           2      0.35         2
3           2     0.419         3
4           2     0.489         4
5           2     0.558         5
...       ...       ...       ...
570         2    46.512       570
571         2    46.581       571
572         2    46.651       572
573         1    46.806       573
574         2    47.059       574
 ... 18 more variables/columns.

2. Use MsBackendRawDiag()

library(rawDiag)
fls <- rep(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'), 1)
be <- backendInitialize(MsBackendRawDiag(), files = fls)
sps_thermofinnigan <- Spectra(be)
sps_thermofinnigan

R> sps_thermofinnigan
MSn data (Spectra) with 574 spectra in a MsBackendRawDiag backend:
      msLevel     rtime scanIndex
    <integer> <numeric> <integer>
1           1     0.097         1
2           2      0.35         2
3           2     0.419         3
4           2     0.489         4
5           2     0.558         5
...       ...       ...       ...
570         2    46.512       570
571         2    46.581       571
572         2    46.651       572
573         1    46.806       573
574         2    47.059       574
 ... 15 more variables/columns.

file(s):
sample.raw
Processing:

R> 

[tobiasko]

Cool!!!

But this statement still confuses me: as.peaklistSet.DataFrame(...)

The above function coerces a peaklistSet object to a DataFrame? Why not simply as.DataFrame(...)? Like date <- as.Date("2017-01-01").

And I am still wondering if there is a more elegant way to initialize the backend. Maybe @lgatto can explain us why the backendInitialize(...) needs a file argument if used for MsBackendDataFrame. DF$fromFile = as.integer(1) looks creepy.

[jorainer]

Nice! But be aware that there will be some quite substantial changes to the MsBackend:

• @files slot will be removed, information about where the data is stored should be provided by the dataStorage spectra variable (and method).
• fromFile will be removed.
• fileNames will be removed.

I am currently finalizing the required changes in the Spectra and fixing/adding unit tests. I'll ping you when it is ready.

[tobiasko]

@jorainer Thx for keeping us in the loop! Is the class definition of Spectra already stable/is it safe to inherit?

[lgatto]

There aren't any major changes to be expected, but some small changes are very possible. If you prefer to wait for a more stable release, I would suggest to wait of a pre-Bioconductor release (I think it is conceivable that we will submit for the next release).

[cpanse]

Cool!!!

But this statement still confuses me: as.peaklistSet.DataFrame(...)

The above function coerces a peaklistSet object to a DataFrame? Why not simply as.DataFrame(...)? Like date <- as.Date("2017-01-01").

@tobiasko this is just S3 cosmetics https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Registering-S3-methods this is just a Hello, World! function. We won't use that S3method.

And I am still wondering if there is a more elegant way to initialize the backend. Maybe @lgatto can explain us why the backendInitialize(...) needs a file argument if used for MsBackendDataFrame. DF$fromFile = as.integer(1) looks creepy.

[tobiasko]

@cpanse Ok, let's discuss coding style issues offline! ;-)

[jorainer]

We recently made some changes in the MsBackend definition:

• @files and @modCount slots are gone.
• Add new spectra variables dataStorage and dataOrigin

The dataStorage is thought to be the replacement for the @files with the difference, that it will return for each spectrum the current storage location (e.g. mzML file, memory, HDF5 file, ...).

I don't expect any major chages anymore in the MsBackend class. I will work now mostly in implementing all missing analysis methods for Spectra.

[cpanse]

@jorainer @lgatto @sgibb; we are on the way shaping a MsBackendRawFileReader package.

Package: MsBackendRawFileReader
Type: Package
Title: Bridging Spectra and ThermoFinnigan raw files
Version: 0.0.1
Authors@R: c(person(given = "Christian",
    family = "Panse", email = "cp@fgcz.ethz.ch", role = c("aut", "cre"),
    comment = c(ORCID = "0000-0003-1975-3064")),
    person(given = "Tobias", family = "Kockmann",
      email = "Tobias.Kockmann@fgcz.ethz.ch", role = "aut", 
    comment = c(ORCID = "0000-0002-1847-885X")))
Depends: R (>= 3.6),
       IRanges,
    methods,
    Spectra,
    rDotNet (>= 0.9)
Suggests:
    knitr,
    testthat
Description: implements an MsBackend for the Spectra package using
  Thermo Fisher Scientific's NewRawFileReader .Net libraries.
  The package is generalizing the functionallity introduced by the
  rawDiag package (Trachsel, 2018 <doi:10.1021/acs.jproteome.8b00173>).
SystemRequirements: mono 4.x or higher on OSX / Linux, .NET 4.x or
        higher on Windows, 'msbuild' and 'nuget' available in the path
URL: https://github.com/cpanse/MsBackendRawFileReader
BugReports: https://github.com/cpanse/MsBackendRawFileReader/issues
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
RoxygenNote: 6.1.1
License: GPL-3
VignetteBuilder: knitr
Collate: 
    'hidden_aliases.R'
    'AllGenerics.R'
    'MsBackendRawFileReader-functions.R'
    'MsBackendRawFileReader.R'
    'zzz.R'

[lgatto]

That's cool.

I had initially the impression that you were using the MsBackendDataFrame as template. You should however rather look at MsBackendMzR for a better fit.

[cpanse]

@lgatto at the moment I am only ctrl-c/ ctrl-v-ing from MsBackendMzR. We have it private for the moment to avoid confusion, but if you wish, we can add you all three to the repository at any time.

[lgatto]

I wouldn't have much time for development at the moment, but would be happy to provide support if needed. I imaging that @jorainer and @sgibb would also contribute important feedback.

[cpanse]

I wouldn't have much time for development at the moment, but would be happy to provide support if needed. I imaging that @jorainer and @sgibb would also contribute important feedback.

@lgatto @jorainer @sgibb we added you to the repo just to enable some transparency and important feedback.