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CentroidR

Repository to centroid profile spectra.

This repository is experimental. Use it at your own risks. Inspired from the original work at https://github.com/EuracBiomedicalResearch/batch_centroid

Requirements

Here is what you minimally need:

  • An mzML file containing profile spectra

Installation

As the package is not (yet) available on CRAN, you will need to install with:

install.packages(
  "CentroidR",
  repos = c(
    "https://adafede.r-universe.dev",
    "https://bioc.r-universe.dev",
    "https://cloud.r-project.org"
  )
)

Use

R 

CentroidR::centroid_one_file(file = "path_to_your/profile/spectra.mzML",
                             pattern = "/profile/",
                             replacement = "/profile_centroided/")
Rscript inst/scripts/centroiding.R --file "path_to_your/profile/spectra.mzML" --pattern "/profile/" --replacement "/profile_centroided/"
Rscript inst/scripts/centroiding.R --help

Docker 

docker pull adafede/centroidr
# docker build . -t adafede/centroidr
 docker run --rm \
  -v path_to_your:/home \
  adafede/centroidr \
  Rscript centroiding.R --file "home/profile/spectra.mzML" --pattern "/profile/" --replacement "/profile_centroided/"

To see all parameters

 docker run --rm \
   -v path_to_your:/home \
  adafede/centroidr \
  Rscript centroiding.R --help

Main Citations

TODO

Others