GetSampleInfo

R Wrapper to the Thermo C# RawFileReader

Installation

To use, you first need to obtain a copy of Thermo's RawFileReader, see details here.

GetSampleInfo requires two Thermo C# assemblies at install time:

• ThermoFisher.CommonCore.Data.dll
• ThermoFisher.CommonCore.RawFileReader.dll

Keep those DLLs outside the repo and point THERMO_RAWFILEREADER_HOME at the directory containing them.

export THERMO_RAWFILEREADER_HOME=/full/path/to/RawFileReader

On macOS and Linux you also need Mono so the C# sources can be compiled and the generated .exe files can be run.

To install, follow the correct instructions here.

mcs --version
Mono C# compiler version 6.8.0.96

With THERMO_RAWFILEREADER_HOME set, package installation will copy the DLLs into inst/bin/RawFileReader/ and compile the C# readers automatically.

R CMD build .
R CMD INSTALL GetSampleInfo_0.4.1.tar.gz

For local development you can also populate the DLLs and compile explicitly:

THERMO_RAWFILEREADER_HOME=/full/path/to/RawFileReader bash inst/compile.sh

If everything has worked there should now be three .exe files in inst/bin/RawFileReader/.

If THERMO_RAWFILEREADER_HOME is not set, or the DLLs cannot be found, the package will still install but the exported functions will fail with a clear runtime error until the readers are compiled.

Usage

> library(GetSampleInfo)

> TestFile <- system.file('extdata/QC01.raw', package = 'GetSampleInfo')

> SampleInfo <- GetSampleInfo(TestFile)

> InstrumentName <- GetInstrumentName(TestFile)
> InstrumentName
$instrument_name
[1] "Thermo Exactive Orbitrap"

$instrument_model
[1] "Exactive Orbitrap"

$instrument_serial
[1] "Exactive slot #1"

> ScanFilters <- GetScanFilters(TestFile)
> ScanFilters 
# A tibble: 2 x 1
  ScanFilter                                
  <chr>                                     
1 FTMS {1,1} - p ESI Full ms [63.00-1000.00]
2 FTMS {1,2} + p ESI Full ms [55.00-1000.00]