Optimization code and documentation for isotope trace (IT) detection in mass spectrometry applications of the Bioconductor package XCMS .
Visualization is the quickest way to optimize IT detection with Massifquant in the XCMS suite. The strategies and methods detailed in:
- optimize-vis-massifquant.Rnw (source code)
- optimize-vis-massifquant.pdf (human readable version)
show how to precisely visualize the effects of parameter variations on the IT detection results. The mouse_data and figs directories correspond to this analysis.
A score-based optimization is possible with a corresponding ground truth annotation of veritable IT sets and a carefully constructed evaluation metric (e.g. f-score). The document
- reproducing-greedy-search-optimization-figures.pdf
details the greedy-search approach as well as how to reproduce the analysis depicted in the Massifquant publication. The compressed folder gate-reproducible.tgz has all the relevant data and scripts to reproduce the entire analysis.