├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── check-bioc.yml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── all-generics.R ├── averaging.R ├── combineAnnotations.R ├── create-database.R ├── createDatabase.R ├── flag-filter-remove.R ├── iw-norm.R ├── matching-algs.R ├── meta_extract.R ├── msPurity.R ├── pcalc.R ├── purityA-0-class.R ├── purityA-av-spectra.R ├── purityA-constructor.R ├── purityA-create-msp.R ├── purityA-filter-frag-spectra.R ├── purityA-frag4feature.R ├── purityA-validate.R ├── purityD-av-spectra.R ├── purityD-class.R ├── purityD-constructor.R ├── purityD-dims-purity.R ├── purityD-fileList.R ├── purityD-filterp.R ├── purityD-subtract.R ├── purityD-writeOut.R ├── purityX-class.R ├── purityX-constructor.R ├── spectral-matching.R ├── spectralMatching.R └── splinepurity.R ├── README.rst ├── inst ├── CITATION └── extdata │ ├── iwqe5.rds │ └── tests │ ├── db │ ├── createDatabase_example.sqlite │ ├── createDatabase_example_OLD.sqlite │ ├── create_database_example.sqlite │ └── metab_compound_subset.sqlite │ ├── external_annotations │ ├── beams.tsv │ ├── combined.tsv │ ├── metfrag.tsv │ ├── probmetab.tsv │ └── sirus_csifingerid.tsv │ ├── msp │ ├── all.msp │ ├── all_OLD.msp │ ├── av_all.msp │ ├── av_all_OLD.msp │ ├── av_all_dupmeta.msp │ ├── av_all_dupmeta_OLD.msp │ ├── av_all_include_adducts.msp │ ├── av_inter.msp │ ├── av_inter_OLD.msp │ ├── av_intra.msp │ ├── av_intra_OLD.msp │ ├── max.msp │ ├── max_OLD.msp │ ├── recrdt.msp │ └── recrdt_OLD.msp │ ├── purityA │ ├── 10_input_filterflagremove.rds │ ├── 1_purityA_pa.rds │ ├── 1_purityA_pa_OLD.rds │ ├── 2_frag4feature_pa.rds │ ├── 2_frag4feature_pa_OLD.rds │ ├── 3_filterFragSpectra_pa.rds │ ├── 3_filterFragSpectra_pa_OLD.rds │ ├── 4_averageIntraFragSpectra_no_filter_pa.rds │ ├── 4_averageIntraFragSpectra_no_filter_pa_OLD.rds │ ├── 5_averageInterFragSpectra_no_filter_pa.rds │ ├── 5_averageInterFragSpectra_no_filter_pa_OLD.rds │ ├── 6_averageAllFragSpectra_no_filter_pa.rds │ ├── 6_averageAllFragSpectra_no_filter_pa_OLD.rds │ ├── 7_averageIntraFragSpectra_with_filter_pa.rds │ ├── 7_averageIntraFragSpectra_with_filter_pa_OLD.rds │ ├── 8_averageInterFragSpectra_with_filter_pa.rds │ ├── 8_averageInterFragSpectra_with_filter_pa_OLD.rds │ ├── 9_averageAllFragSpectra_with_filter_pa.rds │ └── 9_averageAllFragSpectra_with_filter_pa_OLD.rds │ ├── purityX │ ├── 1_purityX_grouped_px.rds │ └── 1_purityX_single_px.rds │ ├── sm │ ├── spectralMatching_result.sqlite │ ├── spectralMatching_result_OLD.sqlite │ └── spectral_matching_result.sqlite │ └── xcms │ ├── ms_only_xcmsnexp.rds │ ├── ms_only_xset_OLD.rds │ ├── msms_only_xcmsnexp.rds │ ├── msms_only_xset.rds │ └── msms_only_xset_OLD.rds ├── man ├── Getfiles.Rd ├── assessPuritySingle.Rd ├── averageAllFragSpectra-purityA-method.Rd ├── averageInterFragSpectra-purityA-method.Rd ├── averageIntraFragSpectra-purityA-method.Rd ├── averageSpectra-purityD-method.Rd ├── averageSpectraSingle.Rd ├── combineAnnotations.Rd ├── createDatabase.Rd ├── createMSP-purityA-method.Rd ├── create_database.Rd ├── dimsPredictPurity-purityD-method.Rd ├── dimsPredictPuritySingle.Rd ├── filterFragSpectra-purityA-method.Rd ├── filterp-purityD-method.Rd ├── flag_remove.Rd ├── frag4feature-purityA-method.Rd ├── getP-purityD-method.Rd ├── get_additional_mzml_meta.Rd ├── groupPeaks-purityD-method.Rd ├── groupPeaksEx.Rd ├── initialize-purityD-method.Rd ├── iwNormGauss.Rd ├── iwNormQE.5.Rd ├── iwNormRcosine.Rd ├── msPurity.Rd ├── pcalc.Rd ├── purityA.Rd ├── purityD-class.Rd ├── purityX.Rd ├── show-purityA-method.Rd ├── show-purityD-method.Rd ├── show-purityX-method.Rd ├── spectralMatching.Rd ├── spectral_matching.Rd ├── subtract-purityD-method.Rd ├── subtractMZ.Rd ├── validate-purityA-method.Rd └── writeOut-purityD-method.Rd ├── msPurity.Rproj ├── tests ├── testthat.R └── testthat │ ├── test.1_pcalc.R │ ├── test.2_purityA.R │ ├── test.2_purityA_OLD.R │ ├── test.3_flagremove.R │ ├── test.4_db.R │ ├── test.4_db_OLD.R │ ├── test.5_sm.R │ ├── test.5_sm_OLD.R │ ├── test.6_combineAnnotations.R │ ├── test.7_purityX.R │ └── test.8_dims.R └── vignettes ├── figure1_analytical_chemistry.jpg ├── figure2_analytical_chemistry.jpg ├── figure3_analytical_chemistry.jpg ├── isolation.png ├── isolation_exp.png ├── msPurity-lcmsms-data-processing-and-spectral-matching-vignette.R ├── msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd ├── msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html ├── msPurity-lcmsms-data-processing-and-spectral-matching-vignette.md ├── msPurity-spectral-database-vignette.R ├── msPurity-spectral-database-vignette.Rmd ├── msPurity-spectral-database-vignette.html ├── msPurity-spectral-database-vignette.md ├── msPurity-vignette.R ├── msPurity-vignette.Rmd ├── msPurity-vignette.html ├── msPurity.Rproj ├── mspurity.bib └── spectral-database-schema.html /.Rbuildignore: 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