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

Here is a generic command in case:

docker run -it --rm -e WINEDEBUG=-all -v .:/data proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert "path_to_your/raw/spectra.wiff" --ignoreUnknownInstrumentError

Note: If using Sciex raw format, use the .wiff and not the .wiff2 for this step!

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

Single file

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/"

Multiple files

"path_to_your/profiles/" |>
    list.files(pattern = ".mzML", full.names = TRUE) |>
    purrr::walk(
      .f = CentroidR::centroid_one_file,
      pattern = "/profiles/",
      replacement = "/profiles_centroided/",
      .progress = TRUE)

Rscript inst/scripts/centroiding.R --directory "path_to_your/profiles/" --pattern "/profiles/" --replacement "/profiles_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/"

 docker run --rm \
  -v path_to_your:/home \
  adafede/centroidr \
  Rscript centroiding.R --directory "home/profiles/" --pattern "/profiles/" --replacement "/profiles_centroided/"

To see all parameters

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

Main Citations

TODO

Others

• The RforMassSpectrometry packages suite: https://doi.org/10.3390/metabo12020173