pyms-test SUMMARY Contains examples of PyMS use given in the User Guide. CONTENT Chapter 2 -- GC-MS data file reading and operations --------- 20a/ -- Reading of GC-MS raw data in the JCAMP-DX format, and some properties of raw data object. The JCAMP-DX file used in this example was generated by GC/MS File Translator Pro (Scientific Instrument Services, Inc) 20b/ -- Reading of GC-MS raw data in the ANDI-MS format, and some properties of raw data object. The ANDI-MS file used in this example was generated by Agilent ChemStation. 20c/ -- Use of data information, info(), function 20d/ -- Illustrates the use of diff() function Chapter 3 -- GC-MS data structure --------- 30a/ -- Demonstrates building of the intensity matrix from the raw GC-MS data, and some basic methods of the IntensityMatrix 30b/ -- Exploration of build intensity matrix parameters. 30c/ -- Build integer mass intensity matrix using bin boundary of -0.3 and +0.7. 31/ -- MassSpectrum and IonChromatogram objects of an IntensityMatrix 32/ -- Saving IonChromatogram and IntensityMatrix information. Chapter 4 -- Data filtering --------- 40a/ -- Trim raw data retention time/scan range 40b/ -- Crop mass range and ignore given masses 41a/ -- Noise filtering with the mean/median moving window filter, on TIC 41b/ -- Noise filtering with the Savitzky-Golay filter, on TIC 42a/, 42b/ -- TopHat baseline correction 43/ -- A pre-processing of data by ICs (building of the intensity matrix, smoothing each IC with the Savitzky-Golay filter and baseline correction with the TopHat corrector) Chapter 5 -- Peaks and Peak detection --------- 50/ -- Demonstrates a Peak object and its properties. 51/ -- Crop mass range and zero mass intensities. 52/ -- Peak detection and deconvolution. 53/ -- Filter list of detected peaks. 54/ -- Peak area. Chapter 6 -- Peak alignment by dynamic programming. --------- 60/ -- Experiment object. 61a/ -- Experiment setup for group A peak data. 61b/ -- Experiment setup for group B peak data. 62/ -- Alignment of group A peaks. 63/ -- Alignment of peaks within group A, group B and between groups A and B. 64/ -- Peak alignment with the "common ion" filtering. Chapter 7 -- Plotting. --------- 70a/ -- A simple plot of TIC 70b/ -- A simple overlay plot of multiple ICs 71/ -- A plot with Display() object. Example shows an overlay plot of TIC, several ICs, and peaks detected by PyMS Chapter 9 -- Parallel processing with PyMS. --------- x10/ -- An example of parallel processing of data. Shows how to loop over all ICs in an intensity matrix, and perform noise smoothing on each IC (in parallel). Please see User Guide for instructions how to run this example on multiple CPUs