To use msconverteR you must have a working installation of Docker. See here for details on how to install.
Once Docker is installed; msconverteR can be installed directly from GitHub
remotes::install_github('wilsontom/msconverteR')
To use msconverteR the chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:latest docker image needs to available. The first time you use msconverteR you should run the get_pwiz_container() function which will pull the image from Docker Hub.
library(msconverteR)
get_pwiz_container()All file conversions are performed by the convert_files function. Conversion parameters are passed to the the msconvert_args parameter in the same way as they would be for msconvert except that the --filter prefix is omitted.
> rawfile <- system.file('QC01.raw',package = 'msconverteR')
> convert_files(rawfile, outpath = NULL, msconvert_args = 'peakPicking true 1-', docker_args = c())
format: mzML
m/z: Compression-None, 64-bit
intensity: Compression-None, 32-bit
rt: Compression-None, 64-bit
ByteOrder_LittleEndian
indexed="true"
outputPath: .
extension: .mzML
contactFilename:
runIndexSet:
spectrum list filters:
peakPicking true 1-
chromatogram list filters:
filenames:
QC01.raw
processing file: QC01.raw
calculating source file checksums
writing output file: .\QC1.mzML