isoorbi

Overview

The goal of the isoorbi R package is to help you process isotopocule measurements from an Orbitrap Isotope Solutions mass spectrometer. It expects .isox files created by IsoX as input.

Installation

You can install the current CRAN version of isoorbi with:

install.packages("isoorbi")

To use the latest updates, you can install the development version of isoorbi from GitHub with:

if(!requireNamespace("pak", quietly = TRUE)) install.packages("pak")
pak::pak("isoverse/isoorbi")

Important: the first time you read a .raw file (this is possible in the development version of isoorbi on GitHub), you will be asked to agree to the License agreement for Thermo’s RawFileReader to proceed.

Show me some code

library(isoorbi)

system.file(package = "isoorbi", "extdata", "testfile_flow.isox") |>
  orbi_read_isox() |>
  orbi_flag_satellite_peaks() |>
  orbi_define_basepeak(basepeak_def = "M0")|> 
  orbi_summarize_results(ratio_method = "sum") |>
  orbi_export_data_to_excel(file = "data_summary.xlsx")

Package layout

Getting help

If you encounter a bug, please file an issue with a minimal reproducible example on GitHub.

For questions and other discussion, please use the isoorbi slack workspace.