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README.md
peak_calling_cwt.R

README.md

R script used for peak calling on the benchmarking dataset as in Dumolin et al. 2019.

Usage:

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:

#m/z int
1998.75 686
1999.17 603
1999.59 640
2000.00 599

Output:
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).

Requirements:

  • 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.

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