├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── C_function.R ├── Global_setting.R ├── MSn_processing.R ├── OptiLCMS_Class.R ├── Optimize_params.R ├── Other_Utils.R ├── Params_db.R ├── Perform_functions.R ├── ROI_Extraction.R ├── RcppExports.R ├── Resume_functions.R ├── Spectra_Infusion_function.R ├── Spectra_Utils.R ├── Spectra_import.R ├── Spectra_visulization.R └── autoconfig.R ├── README.md ├── data └── mSet.rda ├── inst ├── CITATION ├── hmdb │ └── hmdb_all.rds ├── lists │ ├── ions.csv │ ├── neutraladdition.csv │ └── neutralloss.csv ├── rules │ ├── extended_adducts_neg.csv │ ├── extended_adducts_pos.csv │ ├── primary_adducts_neg.csv │ └── primary_adducts_pos.csv └── script │ └── Example_Running_Script.R ├── man ├── CentroidCheck.Rd ├── CentroidMSData.Rd ├── ExecutePlan.Rd ├── Export.Annotation.Rd ├── Export.PeakSummary.Rd ├── Export.PeakTable.Rd ├── FormatInfusionFeatureTable.Rd ├── FormatMSnAnnotation.Rd ├── FormatPeakList.Rd ├── GaussModel.Rd ├── ImportRawMSData.Rd ├── InitDataObjects.Rd ├── InitializaPlan.Rd ├── OptiLCMS.Rd ├── PerformDBSearchingBatch.Rd ├── PerformDDADeconvolution.Rd ├── PerformDIADeconvolution.Rd ├── PerformDataInspect.Rd ├── PerformDataTrimming.Rd ├── PerformIndividualInusionFeatureDection.Rd ├── PerformInfusionImport.Rd ├── PerformInusionFeatureDection.Rd ├── PerformMSnImport.Rd ├── PerformMirrorPlotting.Rd ├── PerformParamsOptimization.Rd ├── PerformPeakAlignment.Rd ├── PerformPeakAnnotation.Rd ├── PerformPeakFiling.Rd ├── PerformPeakPicking.Rd ├── PerformPeakProfiling.Rd ├── PerformROIExtraction.Rd ├── PerformResultsExport.Rd ├── PerformSpectrumConsenus.Rd ├── PlotSpectraBPIadj.Rd ├── PlotSpectraInsensityStistics.Rd ├── PlotSpectraPCA.Rd ├── PlotSpectraRTadj.Rd ├── PlotXIC.Rd ├── SetAnnotationParam.Rd ├── SetGlobalParallel.Rd ├── SetPeakParam.Rd ├── SetPlotParam.Rd ├── UpdateRawfiles.Rd ├── calculate_entropy_similarity.Rd ├── calculate_unweighted_entropy_similarity.Rd ├── mSet.Rd ├── plotBPIs.Rd ├── plotMSfeature.Rd ├── plotSingleTIC.Rd ├── plotTICs.Rd ├── running.plan.Rd └── updateRawSpectraPath.Rd ├── src ├── CleanSpectrum.c ├── CleanSpectrum.h ├── DecoSpectra.cpp ├── DecoSpectra.h ├── DetectPeaks.cpp ├── DetectPeaks.h ├── Makevars ├── Makevars.win ├── PerformDDAProcess.cpp ├── PerformDDAProcess.h ├── PerformDIAProcess.cpp ├── PerformDIAProcess.h ├── RcppExports.cpp ├── SWATH_DIA_Deconv.cpp ├── SpectralEntropy.c ├── SpectralEntropy.h ├── binarySearch.h ├── dda_utilities.cpp ├── dda_utilities.h ├── decorana.f ├── entropy.cpp ├── entropy.h ├── export_interfece.cpp ├── fastMatch.c ├── fastMatch.h ├── fastcluster.h ├── hclust_ultrafast.cpp ├── hclust_ultrafast.h ├── init.c ├── linear_regression.cpp ├── linear_regression.h ├── lowess.cpp ├── lowess.h ├── massifquant │ ├── DataKeeper.cpp │ ├── DataKeeper.h │ ├── OpOverload.cpp │ ├── OpOverload.h │ ├── SegProc.cpp │ ├── SegProc.h │ ├── TrMgr.cpp │ ├── TrMgr.h │ ├── Tracker.cpp │ ├── Tracker.h │ ├── dpq.h │ ├── nmath.h │ └── xcms_massifquant.cpp ├── mzClust.cpp ├── mzROI.c ├── obiwarp │ ├── lmat.h │ ├── mat.cpp │ ├── mat.h │ ├── vec.cpp │ ├── vec.h │ ├── xcms_dynprog.cpp │ ├── xcms_dynprog.h │ └── xcms_lmat.cpp ├── optim_src.h ├── optim_ultra.cpp ├── optim_ultra.h ├── pense │ ├── alias.hpp │ ├── autoconfig.hpp │ ├── cd_pense.hpp │ ├── constants.hpp │ ├── container_utility.hpp │ ├── enpy_initest.cc │ ├── enpy_initest.hpp │ ├── enpy_psc.cc │ ├── enpy_psc.hpp │ ├── enpy_types.hpp │ ├── m_loss.hpp │ ├── nsoptim.hpp │ ├── nsoptim │ │ ├── armadillo.hpp │ │ ├── armadillo_forward.hpp │ │ ├── config.hpp │ │ ├── container.hpp │ │ ├── container │ │ │ ├── data.hpp │ │ │ ├── forward.hpp │ │ │ ├── metrics.hpp │ │ │ └── regression_coefficients.hpp │ │ ├── objective.hpp │ │ ├── objective │ │ │ ├── adaptive_en_penalty.hpp │ │ │ ├── convex.hpp │ │ │ ├── en_penalty.hpp │ │ │ ├── forward.hpp │ │ │ ├── loss.hpp │ │ │ ├── ls_regression_loss.hpp │ │ │ └── penalty.hpp │ │ ├── optimizer.hpp │ │ ├── optimizer │ │ │ ├── admm.hpp │ │ │ ├── auglars.hpp │ │ │ ├── coordinate_descent.hpp │ │ │ ├── dal.hpp │ │ │ ├── dal_helper.hpp │ │ │ ├── linear_algebra_utilities.hpp │ │ │ ├── mm.hpp │ │ │ ├── optimizer_base.hpp │ │ │ ├── optimum.hpp │ │ │ └── soft_threshold.hpp │ │ ├── rcpp_integration.hpp │ │ ├── traits │ │ │ ├── can_evaluate.hpp │ │ │ ├── can_optimize.hpp │ │ │ ├── has_convex_surrogate.hpp │ │ │ ├── has_difference_op.hpp │ │ │ ├── is_adaptive.hpp │ │ │ ├── is_differentiable.hpp │ │ │ ├── is_en_penalty.hpp │ │ │ ├── is_iterative_algorithm.hpp │ │ │ ├── is_loss_function.hpp │ │ │ ├── is_ls_regression_loss.hpp │ │ │ ├── is_penalty_function.hpp │ │ │ ├── is_weighted.hpp │ │ │ ├── sfinae_types.hpp │ │ │ └── traits.hpp │ │ └── utilities.hpp │ ├── nsoptim_forward.hpp │ ├── omp_utils.hpp │ ├── r_en_regression.cc │ ├── r_en_regression.hpp │ ├── r_enpy.cc │ ├── r_enpy.hpp │ ├── r_interface.cc │ ├── r_interface_utils.cc │ ├── r_interface_utils.hpp │ ├── r_mesten_regression.cc │ ├── r_mesten_regression.hpp │ ├── r_pense_regression.cc │ ├── r_pense_regression.hpp │ ├── r_robust_utils.cc │ ├── r_robust_utils.hpp │ ├── r_utilities.cc │ ├── r_utilities.hpp │ ├── rcpp_integration.hpp │ ├── rcpp_parse_config.cc │ ├── rcpp_parse_config.hpp │ ├── rcpp_utils.hpp │ ├── rcpp_utils_forward.hpp │ ├── regularization_path.hpp │ ├── regularization_path_new.hpp │ ├── rho.cc │ ├── rho.hpp │ ├── robust_scale_location.cc │ ├── robust_scale_location.hpp │ └── s_loss.hpp ├── rules.h ├── spectra_searching.cpp ├── spectrumConsensus.cpp ├── sqlite │ ├── shell.c │ ├── sqlite3.c │ ├── sqlite3.h │ └── sqlite3ext.h ├── sqlite_utilities.cpp ├── sqlite_utilities.h ├── util.cpp ├── utilities.cpp ├── utilities.h ├── xcms_binners.c ├── xcms_binners.h └── xcms_obiwarp.cpp └── vignettes └── OptiLCMS_MS1.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xia-lab/OptiLCMS/HEAD/.Rbuildignore 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