Man pages for xia-lab/OptiLCMS
Optimized LC-MS Spectra Processing
| calculate_entropy_similarity | Entropy similarity between two spectra |
| calculate_unweighted_entropy_similarity | Unweighted entropy similarity between two spectra |
| CentroidCheck | CentroidCheck |
| CentroidMSData | CentroidMSData |
| ExecutePlan | ExecutePlan |
| Export.Annotation | Export.Annotation |
| Export.PeakSummary | Export.PeakSummary |
| Export.PeakTable | Export.PeakTable |
| FormatMSnAnnotation | Title |
| FormatPeakList | Format Peak List |
| GaussModel | GaussModel |
| ImportRawMSData | Import raw MS data |
| InitDataObjects | InitDataObjects |
| InitializaPlan | Initializing running plan |
| mSet | LC/MS data mSet object example |
| OptiLCMS | OptiLCMS: A package for computating the notorious bar... |
| PerformDataInspect | PerformDataInspect |
| PerformDataTrimming | Perform ROI Extraction from raw MS data (PerformDataTrimming) |
| PerformDBSearchingBatch | PerformDBSearchingBatch |
| PerformDDADeconvolution | PerformDDADeconvolution |
| PerformDIADeconvolution | PerformDIADeconvolution |
| PerformMirrorPlotting | PerformMirrorPlotting |
| PerformMSnImport | PerformMSnImport |
| PerformParamsOptimization | Perform Parameters Optimization |
| PerformPeakAlignment | PerformPeakAlignment |
| PerformPeakAnnotation | Perform peak annotation |
| PerformPeakFiling | PerformPeakFiling |
| PerformPeakPicking | PerformPeakPicking |
| PerformPeakProfiling | Perform peak profiling |
| PerformResultsExport | PerformResultsExport |
| PerformROIExtraction | Perform ROI Extraction from raw MS data |
| PerformSpectrumConsenus | PerformSpectrumConsenus |
| plotBPIs | plotBPIs |
| plotMSfeature | plotMSfeature |
| plotSingleTIC | plotSingleTIC |
| PlotSpectraBPIadj | PlotSpectraBPIadj |
| PlotSpectraInsensityStistics | PlotSpectraInsensityStistics |
| PlotSpectraPCA | PlotSpectraPCA |
| PlotSpectraRTadj | PlotSpectraRTadj |
| plotTICs | plotTICs |
| PlotXIC | PlotXIC/EIC |
| running.plan | running.plan |
| SetAnnotationParam | Set annotation parameters |
| SetGlobalParallel | SetGlobalParallel |
| SetPeakParam | Set parameters for peak profiling and parameters optimization |
| SetPlotParam | SetPlotParam |
| UpdateRawfiles | UpdateRawfiles |
| updateRawSpectraPath | updateRawSpectraPath |
