addAxes | addAxes |
addXLab | addXLab add an x-axis label shifted by marginShift from... |
addYLab | addYLab add an y-axis label shifted by marginShift from... |
auc | Area Under the Curve of the Reciever Operating Curve |
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... |
expandRange | expandRange expand a range by a relative factor. |
fixFileExt | fixFileExt |
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 |
getFileExt | getFileExt |
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 |
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