API for xia-lab/OptiLCMS
Optimized LC-MS Spectra Processing
| Global functions | |
|---|---|
| .CentroidSpectra | Source code |
| .aggregateMethod2int | Source code |
| .applyRtAdjToChromPeaks | Source code |
| .applyRtAdjustment | Source code |
| .createProfileMatrix | Source code |
| .emptyscan.remove | Source code |
| .exportmSetRuleClass | Source code |
| .feature_values | Source code |
| .get.current.plan | Source code |
| .get.rdt.set | Source code |
| .getChromPeakData | Source code |
| .getDataPath | Source code |
| .getDdaMS2Scans | Source code |
| .getPeakGroupsRtMatrix | Source code |
| .get_closest_index | Source code |
| .groupval | Source code |
| .insertColumn | Source code |
| .match_trim_vector_index | Source code |
| .match_trim_vectors | Source code |
| .narrow_rt_boundaries | Source code |
| .on.public.web | Source code |
| .peakIndex | Source code |
| .perform.fast.univ.tests | Source code |
| .rawMat | Source code |
| .replace.by.lod | Source code |
| .set.rdt.set | Source code |
| .testReadMSDataInput | Source code |
| CachePathCorrection | Source code |
| CentroidCheck | Man page Source code |
| CentroidMSData | Man page Source code |
| ColMax | Source code |
| CommandOrganize | Source code |
| CommandsVerify | Source code |
| ComputeEncasing | Source code |
| ContaminatsRemoval | Source code |
| DecoSpectra | Source code |
| Densitygrouping_slave | Source code |
| DescendMin | Source code |
| DescendZero | Source code |
| DescendZeroR | Source code |
| DetectMS2Design | Source code |
| ExecutePlan | Man page Source code |
| ExperimentsCluster_doe | Source code |
| Export.Annotation | Man page Source code |
| Export.PeakSummary | Man page Source code |
| Export.PeakTable | Man page Source code |
| FastRunningShow_auto | Source code |
| FastRunningShow_customized | Source code |
| FilesInclusion_identifier | Source code |
| FindEqualGreaterM | Source code |
| FormatMSnAnnotation | Man page Source code |
| FormatPeakList | Man page Source code |
| GaussModel | Man page |
| GeneratePeakList | Source code |
| GetDist3D | Source code |
| GetRGBColorGradient | Source code |
| ImportRawMSData | Man page Source code |
| InitDataObjects | Man page Source code |
| InitializaPlan | Man page Source code |
| MSW.extendLength | Source code |
| MSW.extendNBase | Source code |
| MSW.getLocalMaximumCWT | Source code |
| MSW.getRidge | Source code |
| MessageOutput | Source code |
| MirrorPlotting | Source code |
| OptiChromPeaks | Source code |
| OptiLCMS | Man page |
| ParamsChanged | Source code |
| Path2Files | Source code |
| PeakGroupCV | Source code |
| PeakPicking_Massifquant_slave | Source code |
| PeakPicking_MatchedFilter_slave | Source code |
| PeakPicking_centWave_slave | Source code |
| PeakPicking_core | Source code |
| PeakPicking_prep | Source code |
| PerformAsariResultsFormating | Source code |
| PerformBlankSubstraction | Source code |
| PerformDBSearchingBatch | Man page Source code |
| PerformDDADeco | Source code |
| PerformDDADeconvolution | Man page Source code |
| PerformDIADeco | Source code |
| PerformDIADeconvolution | Man page Source code |
| PerformDIA_main | Source code |
| PerformDataInspect | Man page Source code |
| PerformDataTrimming | Man page Source code |
| PerformFastUnivTests | Source code |
| PerformFormulaGeneration | Source code |
| PerformMSDataOutput | Source code |
| PerformMSnImport | Man page Source code |
| PerformMassMatching | Source code |
| PerformMirrorPlotting | Man page Source code |
| PerformParamsOptimization | Man page Source code |
| PerformPeakAlignment | Man page Source code |
| PerformPeakAnnotation | Man page Source code |
| PerformPeakFiling | Man page Source code |
| PerformPeakGrouping | Source code |
| PerformPeakPicking | Man page Source code |
| PerformPeakProfiling | Man page Source code |
| PerformROIExtraction | Man page Source code |
| PerformRTcorrection | Source code |
| PerformResultsExport | Man page Source code |
| PerformSpectrumConsenus | Man page Source code |
| PlotSpectraBPIadj | Man page Source code |
| PlotSpectraInsensityStistics | Man page Source code |
| PlotSpectraPCA | Man page Source code |
| PlotSpectraRTadj | Man page Source code |
| PlotXIC | Man page Source code |
| RT.Adjust_peakGroup | Source code |
| R_set_obiwarpR | Source code |
| RectUnique | Source code |
| SSgaussStats | Source code |
| SanitySpectra | Source code |
| SetAnnotationParam | Man page Source code |
| SetGlobalParallel | Man page Source code |
| SetPeakParam | Man page Source code |
| SetPlotParam | Man page Source code |
| SlaveCluster_doe | Source code |
| SpectraClean | Source code |
| SpectraDeconvCore | Source code |
| SpectraSearching | Source code |
| SpectraSearchingBatch | Source code |
| SpectraSearchingSingle | Source code |
| SpectrumConsensus | Source code |
| Statistic_doe | Source code |
| UpdateRawfiles | Man page Source code |
| WhichColMax | Source code |
| addFragments | Source code |
| adjustRtimeSubset | Source code |
| adjustRtime_obiwarp | Source code |
| adjustRtime_peakGroup | Source code |
| annotateGrp | Source code |
| annotation_export | Source code |
| attachList | Source code |
| binYonXR | Source code |
| breaks_on_nBinsR | Source code |
| cache.read | Source code |
| cache.save | Source code |
| calcCV | Source code |
| calcCiS | Source code |
| calcGaussianS | Source code |
| calcIsotopeMatrix | Source code |
| calcMaximumCarbon | Source code |
| calcPC.hcs | Source code |
| calcPPS2 | Source code |
| calcRCS_GSValues | Source code |
| calculatePPKs | Source code |
| calculateSet_doe | Source code |
| calculate_entropy_similarity | Man page Source code |
| calculate_unweighted_entropy_similarity | Man page Source code |
| cent | Source code |
| checkHypothese | Source code |
| checkIntensitiesAtRtBoundaries | Source code |
| checkIps | Source code |
| checkIsotopes | Source code |
| checkNormalDistribution | Source code |
| checkOidCausality | Source code |
| checkParams | Source code |
| checkQuasimolion | Source code |
| checkSinusDistribution | Source code |
| checkfac | Source code |
| combineCalc | Source code |
| combineParams | Source code |
| continuousPtsAboveThreshold | Source code |
| continuousPtsAboveThresholdIdx | Source code |
| continuousPtsAboveThresholdIdxR | Source code |
| continuousPtsAboveThresholdR | Source code |
| controller.modifier | Source code |
| controller.resetter | Source code |
| creatPeakTable | Source code |
| create.matrix | Source code |
| createHypothese | Source code |
| createModel | Source code |
| decode | Source code |
| decodeAll | Source code |
| descendMinR | Source code |
| descendMinTol | Source code |
| dia_feature_preparation | Source code |
| encode | Source code |
| envir.save | Source code |
| estimatePPM | Source code |
| estimateSNThresh | Source code |
| expand.grid.subset | Source code |
| extFUN | Source code |
| extractPeakForGaussian | Source code |
| fast.write.csv | Source code |
| fastMatchR | Source code |
| featureSUM | Source code |
| filterPeaksfromNoise | Source code |
| filterPpmError | Source code |
| filtfft | Source code |
| findAdducts | Source code |
| findEqualGreaterMR | Source code |
| findIsotopes.CAMERA | Source code |
| findIsotopes.IPO | Source code |
| findIsotopesPspec | Source code |
| findTruePeaks | Source code |
| find_matches | Source code |
| findmzROIR | Source code |
| fitGauss | Source code |
| formatFileSpectrumNames | Source code |
| gauss | Source code |
| gaussCoverage | Source code |
| generateMS2dbOpt_optilcms | Source code |
| generatePvals_SigFeatures | Source code |
| getAllPeakEICs | Source code |
| getCcdParameter | Source code |
| getClusterType | Source code |
| getEIC4Peaks | Source code |
| getEICR | Source code |
| getIntensitiesFromRawdata | Source code |
| getLocalNoiseEstimate | Source code |
| getMZR | Source code |
| getMaxSettings | Source code |
| getMaximumLevels | Source code |
| getPeaklist | Source code |
| getPeaks_selection | Source code |
| getRGTVValues | Source code |
| get_reference_sample_id | Source code |
| getderivativeIons | Source code |
| groupval | Source code |
| imputeLinInterpol | Source code |
| info.save | Source code |
| is.wholenumber | Source code |
| isCdfFile | Source code |
| jobFinished | Source code |
| joinOverlappingPeaks | Source code |
| mSet | Man page |
| mSet.obiwarp | Source code |
| mSet2xcmsSet | Source code |
| marker_record | Source code |
| massDiffMatrix | Source code |
| massifquantROIs | Source code |
| mpi.comm.size | Source code |
| my.col2rgba | Source code |
| my.json.scatter | Source code |
| mz.trim_random | Source code |
| mz.trim_specific | Source code |
| na.flatfill | Source code |
| naOmit | Source code |
| normalize_spectrum | Source code |
| optimize.xcms.doe | Source code |
| optimizxcms.doe.peakpicking | Source code |
| parse_ms2peaks | Source code |
| peakTableSUM | Source code |
| peaks_IPO | Source code |
| peakwidth_est | Source code |
| perform.command | Source code |
| perform.plan | Source code |
| plot.MS_3D | Source code |
| plotBPIs | Man page Source code |
| plotMSfeature | Man page Source code |
| plotSingleTIC | Man page Source code |
| plotTICs | Man page Source code |
| ppmEstCore | Source code |
| ppm_diff | Source code |
| process_project | Source code |
| profMat | Source code |
| profiling_param_identifier | Source code |
| read.InMemMSd.data | Source code |
| read.MSdata | Source code |
| read.OnDiskMS.data | Source code |
| readLists | Source code |
| recordMarker_resetter | Source code |
| recording_identifier | Source code |
| rectUniqueR | Source code |
| resolveFragmentConnections | Source code |
| resultIncreased_doe | Source code |
| rgba_to_hex_opacity | Source code |
| rowcolFt | Source code |
| rowcoltt | Source code |
| rt.trim_random | Source code |
| rt.trim_specific | Source code |
| run_process | Source code |
| running.plan | Man page Source code |
| sampclass | Source code |
| scale_range | Source code |
| setCacheEnv | Source code |
| setDefaultLists | Source code |
| ssm_trim | Source code |
| testCacheArg | Source code |
| testNormalDistribution | Source code |
| testSinusDistribution | Source code |
| trimm | Source code |
| typeCastParams | Source code |
| updateRawSpectraPath | Man page Source code |
| valueCount2ScanIndex | Source code Source code |
