Man pages for IFIproteomics/LFQbench
Label Free Quantitation benchmark package

addAxesaddAxes
addXLabaddXLab add an x-axis label shifted by marginShift from...
addYLabaddYLab add an y-axis label shifted by marginShift from...
avgNAavgNA
avg_top_nsum_top_n
createNumericPairscreateNumericPairs
emptyPlotemptyPlot show an empty plot with the plotting area in given...
evalCommandLineArgumentsevalCommandLineArguments This function evaluates the...
FSWE.addModificationFSWE.addModification
FSWE.addSoftwareConfigurationFSWE.addSoftwareConfiguration
FSWE.generateReportsFSWE.generateReports
FSWE.initConfigurationFSWE.initConfiguration
FSWE.init.defaultSoftwaresto be called from init
FSWE.listModificationsFSWE.listModifications
FSWE.scaleIntensitiesFSWE.scaleIntensities
FSWE.setDatasetInjectionNamesFSWE.setDatasetInjectionNames
FSWE.setSpeciesTagsFSWE.setSpeciesTags
FSWE.simExperimentFSWE.simExperiment
FSWE.switchSoftwareConfigurationFSWE.switchSoftwareConfiguration
getCombinedLogRatiosgetCombinedLogRatios
getCombinedProteinRSDsgetCombinedProteinRSDs
getOutlierIdxgetOutlierIdx get outlier indices out of a range defined as...
getQuantileAccuracygetQuantileAccuracy
getQuantilePrecisiongetQuantilePrecision
getQuantileSeparationgetQuantileSeparation
getRangedAccuracygetRangeAccuracy
getRangedPrecisiongetRangePrecision
getRangedSepRategetRangedSepRate
getSepRategetSepRate
guessOrganismguessOrganism
guessSepguessSep This function assigns a separator for separated...
guessSoftwareSourceguessSoftwareSource
LFQbench.batchProcessFilesLFQbench.batchProcessFiles
LFQbench.batchProcessRootFolderLFQbench.batchProcessRootFolder
LFQbench.changeConfigurationLFQbench.changeConfiguration
LFQbench.explainMetricsLFQbench.explainMetrics
LFQbench.getMetricsLFQbench.getMetrics
LFQbench.initConfigurationLFQbench.initConfiguration
LFQbench.plotProteinDispersionBySampleLFQbench.plotProteinDispersionBySample
LFQbench.plotProteinDispersionBySpeciesLFQbench.plotProteinDispersionBySpecies
LFQbench.plotResultSetLFQbench.plotResultSet
LFQbench.plotSampleCompositionLFQbench.plotSampleComposition
LFQbench.plotSpeciesLegendsLFQbench.plotSpeciesLegends
LFQbench.plotToFileLFQbench.plotToFile
LFQbench.processConfigrecalculate some parameters from user defined configuration
LFQbench.processDocSetLFQbench.processDocSet
LFQbench.processFileLFQbench.processFile
LFQbench.setDataRootFolderLFQbench.setDataRootFolder
LFQbench.showAllSpeciesQCLFQbench.showAllSpeciesQC
LFQbench.showDistributionDensityPlotLFQbench.showDistributionDensityPlot
LFQbench.showLogRatioBoxPlotLFQbench.showLogRatioBoxPlot
LFQbench.showMetricsLFQbench.showMetrics
LFQbench.showQuantBarPlotLFQbench.showQuantBarPlot
LFQbench.showScatterAndBoxPlotLFQbench.showScatterAndBoxPlot
LFQbench.showScatterAndDensityPlotLFQbench.showScatterAndDensityPlot
LFQbench.showScatterPlotLFQbench.showScatterPlot
LFQbench.showSingleSpeciesQCLFQbench.showSingleSpeciesQC
loadLibraryloadLibrary install and load a library
logIdStatisticslogIdStatistics
makeDocSetmakeDocSet
makeEverythingInOneFolderDocSetmakeEverythingInOneFolderDocSet
makeScattermakeScatter
median_allmedian_all
median_quenchmedian_quench
mkdirmkdir This recursively create a directory if it does not...
moveFilesmoveFiles
plotSpeciesLegendplotSpeciesLegend
qboxplotqboxplot This boxplots for matrix columns or list of vectors...
rmsrms
saveIDssaveIDs
saveLogRatiossaveLogRatios
saveMetricssaveMetrics
saveSampleCVssaveSampleCVs
saveSampleMeanssaveSampleMeans
saveSpeciesSeparationsaveSpeciesSeparation
single_hitssingle_hits
spinerspiner
stopHerestopHere A stop with no error messages
sumNAsumNA
sum_top_nsum_top_n
take1stentrytake1stentry
IFIproteomics/LFQbench documentation built on Jan. 9, 2018, 8:02 a.m.