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