R script used for peak calling on the benchmarking dataset as in Dumolin et al. 2019.
Rscript peak_calling_cwt.R FullMS_directory
where FullMS_directory is the name of a directory containing .txt files of quality filtered, raw mass spectra. Each text file should have two tab-spearated columns without headers. First column is the m/z value and second column the intensity value as in the example below:
Output is stored in the PKL4DICE directory. The directory contains the peak lists for each spectrum as called by the MassSpectWavelet package (1 file per spectrum).
- Rscript version 3.4.4 or newer (not tested on older versions)
- MassSpecWavelet package version 1.48.1, available from Bioconductor (Du et al. 2006)
References: Du P, Kibbe WA, Lin SM (2006). “Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.” Bioinformatics, 22, 2059-2065.