OptiLCMS is an R package providing an optimized LC-MS raw data processing workflow. The source code of the "MS Spectral Processing" Module in MetaboAnalyst is contained here. OptiLCMS can be used to repeat the results generated by MetaboAnalyst at local, and is also optionally dependent by MetaboAnalystR to perform raw MS data processing.
There are 3 typical approaches provided for users to install this package as below.
# Latest features could only be obtained from this approach, make sure 'devtools' installed first
devtools::install_github("xia-lab/OptiLCMS", build = TRUE, build_vignettes = FALSE, build_manual =TRUE)
Download the latest version from the following Options:
# Remember to replace the PATH_TO_TAR as the right path of your downloaded package (OptiLCMS_1.1.X.tar.gz).
install.packages(PATH_TO_TAR, repos = NULL, type="source")
A step-by-step tutorial will be prepared for users to start their analysis by following them (available soon).
OptiLCMS package has been developed by the XiaLab at McGill University. If you use the R package, please cite us:
- Pang, Z., Chong, J., Li, S. and Xia, J. (2020) MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics. Metabolites 10(5) 186 link
From within R:
citation("OptiLCMS")To inform us of any bugs or requests, please open a new issue (and @ Zhiqiang-PANG !!) or send an email to zhiqiang.pang@mail.mcgill.ca.