Man pages for IFIproteomics/LFQbench
Label Free Quantitation benchmark package
| addAxes | addAxes |
| addXLab | addXLab add an x-axis label shifted by marginShift from... |
| addYLab | addYLab add an y-axis label shifted by marginShift from... |
| avgNA | avgNA |
| avg_top_n | sum_top_n |
| createNumericPairs | createNumericPairs |
| emptyPlot | emptyPlot show an empty plot with the plotting area in given... |
| evalCommandLineArguments | evalCommandLineArguments This function evaluates the... |
| FSWE.addModification | FSWE.addModification |
| FSWE.addSoftwareConfiguration | FSWE.addSoftwareConfiguration |
| FSWE.generateReports | FSWE.generateReports |
| FSWE.initConfiguration | FSWE.initConfiguration |
| FSWE.init.defaultSoftwares | to be called from init |
| FSWE.listModifications | FSWE.listModifications |
| FSWE.scaleIntensities | FSWE.scaleIntensities |
| FSWE.setDatasetInjectionNames | FSWE.setDatasetInjectionNames |
| FSWE.setSpeciesTags | FSWE.setSpeciesTags |
| FSWE.simExperiment | FSWE.simExperiment |
| FSWE.switchSoftwareConfiguration | FSWE.switchSoftwareConfiguration |
| getCombinedLogRatios | getCombinedLogRatios |
| getCombinedProteinRSDs | getCombinedProteinRSDs |
| getOutlierIdx | getOutlierIdx get outlier indices out of a range defined as... |
| getQuantileAccuracy | getQuantileAccuracy |
| getQuantilePrecision | getQuantilePrecision |
| getQuantileSeparation | getQuantileSeparation |
| getRangedAccuracy | getRangeAccuracy |
| getRangedPrecision | getRangePrecision |
| getRangedSepRate | getRangedSepRate |
| getSepRate | getSepRate |
| guessOrganism | guessOrganism |
| guessSep | guessSep This function assigns a separator for separated... |
| guessSoftwareSource | guessSoftwareSource |
| LFQbench.batchProcessFiles | LFQbench.batchProcessFiles |
| LFQbench.batchProcessRootFolder | LFQbench.batchProcessRootFolder |
| LFQbench.changeConfiguration | LFQbench.changeConfiguration |
| LFQbench.explainMetrics | LFQbench.explainMetrics |
| LFQbench.getMetrics | LFQbench.getMetrics |
| LFQbench.initConfiguration | LFQbench.initConfiguration |
| LFQbench.plotProteinDispersionBySample | LFQbench.plotProteinDispersionBySample |
| LFQbench.plotProteinDispersionBySpecies | LFQbench.plotProteinDispersionBySpecies |
| LFQbench.plotResultSet | LFQbench.plotResultSet |
| LFQbench.plotSampleComposition | LFQbench.plotSampleComposition |
| LFQbench.plotSpeciesLegends | LFQbench.plotSpeciesLegends |
| LFQbench.plotToFile | LFQbench.plotToFile |
| LFQbench.processConfig | recalculate some parameters from user defined configuration |
| LFQbench.processDocSet | LFQbench.processDocSet |
| LFQbench.processFile | LFQbench.processFile |
| LFQbench.setDataRootFolder | LFQbench.setDataRootFolder |
| LFQbench.showAllSpeciesQC | LFQbench.showAllSpeciesQC |
| LFQbench.showDistributionDensityPlot | LFQbench.showDistributionDensityPlot |
| LFQbench.showLogRatioBoxPlot | LFQbench.showLogRatioBoxPlot |
| LFQbench.showMetrics | LFQbench.showMetrics |
| LFQbench.showQuantBarPlot | LFQbench.showQuantBarPlot |
| LFQbench.showScatterAndBoxPlot | LFQbench.showScatterAndBoxPlot |
| LFQbench.showScatterAndDensityPlot | LFQbench.showScatterAndDensityPlot |
| LFQbench.showScatterPlot | LFQbench.showScatterPlot |
| LFQbench.showSingleSpeciesQC | LFQbench.showSingleSpeciesQC |
| loadLibrary | loadLibrary install and load a library |
| logIdStatistics | logIdStatistics |
| makeDocSet | makeDocSet |
| makeEverythingInOneFolderDocSet | makeEverythingInOneFolderDocSet |
| makeScatter | makeScatter |
| median_all | median_all |
| median_quench | median_quench |
| mkdir | mkdir This recursively create a directory if it does not... |
| moveFiles | moveFiles |
| plotSpeciesLegend | plotSpeciesLegend |
| qboxplot | qboxplot This boxplots for matrix columns or list of vectors... |
| rms | rms |
| saveIDs | saveIDs |
| saveLogRatios | saveLogRatios |
| saveMetrics | saveMetrics |
| saveSampleCVs | saveSampleCVs |
| saveSampleMeans | saveSampleMeans |
| saveSpeciesSeparation | saveSpeciesSeparation |
| single_hits | single_hits |
| spiner | spiner |
| stopHere | stopHere A stop with no error messages |
| sumNA | sumNA |
| sum_top_n | sum_top_n |
| take1stentry | take1stentry |
