API for eahrne/SafeQuant
A Toolbox for the Analysis of Proteomics Data

Global functions
COLORS Man page
addIdQvalues Man page Source code
addPTMCoord Source code
addScaffoldPTMFAnnotations Man page Source code
allpValueHist Source code
barplotMSSignal Man page Source code
correlationPlot Source code
createExpDesign Man page Source code
createExpressionDataset Man page Source code
createPairedExpDesign Man page Source code
cvBoxplot Man page Source code
cysteinFreqBarplot Man page Source code
dOverviewPlots Source code
dPlots Source code
dotColorstrip Source code
dotProduct Man page Source code
errorBar Source code
exp2Exprs Source code
expDesignTagToExpDesign Man page Source code
export Man page Source code
filterSQA Source code
getAAProteinCoordinates Man page Source code
getAccessionNumber Man page Source code
getAllCV Man page Source code
getAllDotProduct Man page Source code
getAllEBayes Man page Source code
getBaselineIntensity Man page Source code
getCV Man page Source code
getCalibMixEset Source code
getCalibMixPairedEset Source code
getConditionColors Source code
getControlCondition Source code
getExpDesignProgenesisCsv Man page Source code
getFTestPValue Man page Source code
getFileType Source code
getFirstEntry Source code
getGeneName Man page Source code
getGlobalNormFactors Man page Source code
getGoTermDF Man page Source code
getIBAQEset Man page Source code
getIdLevelQvals Man page Source code
getImpuritiesMatrix Man page Source code
getImputationMatrix Man page Source code
getIntSumPerProtein Man page Source code
getKinaseFreq Man page Source code
getKinases Man page Source code
getLOD Man page Source code
getLoocvFoldError Man page Source code
getMaxIndex Man page Source code
getMeanCenteredRange Man page Source code
getModifProteinCoordinates Man page Source code
getMotifFreq Man page Source code
getMotifX Man page Source code
getNAFraction Man page Source code
getNbDetectablePeptides Man page Source code
getNbMisCleavages Man page Source code
getNbPeptidesPerProtein Man page Source code
getNbPlex Source code
getNbRolledUpFeatures Man page Source code
getNbSpectraPerProtein Man page Source code
getPeptides Man page Source code
getProgenesisCsvExpressionColIndices Source code
getProteaseRegExp Source code
getRTNormFactors Man page Source code
getRatios Man page Source code
getScoreCutOff Man page Source code
getSignalPerCondition Man page Source code
getSkipLineNb Source code
getSwaths Man page Source code
getTopX Man page Source code
getUniquePtmMotifs Source code
getUserOptions Man page Source code
ggDilutionCurve Man page Source code
ggVolcanoPlot Man page Source code
globalNormalize Man page Source code
hClustHeatMap Man page Source code
isCon Man page Source code
isDecoy Man page Source code
isStrippedACs Man page Source code
kinaseMotif Man page
log2Exprs Source code
maPlotSQ Man page Source code
missinValueBarplot Man page Source code
ntensityAdjustment Source code
option_list Man page
outerLegend Source code
pairsAnnot Man page Source code
parseCSV Source code
parseMaxQuantProteinGroupTxt Man page Source code
parseProgenesisFeatureCsv Man page Source code
parseProgenesisPeptideMeasurementCsv Man page Source code
parseProgenesisProteinCsv Man page Source code
parseScaffoldPTMReport Man page Source code
parseScaffoldRawFile Man page Source code
perFeatureNormalization Man page Source code
plot.safeQuantAnalysis Source code
plotAbsEstCalibrationCurve Man page Source code
plotAdjustedVsNonAdjustedRatio Man page Source code
plotAllGGVolcanoes Man page Source code
plotCalibrationCurve Source code
plotExpDesign Man page Source code
plotIdScoreVsFDR Man page Source code
plotLogo Man page Source code
plotMSSignalDistributions Man page Source code
plotNbIdentificationsVsRT Man page Source code
plotNbValidDeFeaturesPerFDR Man page Source code
plotPrecMassErrorDistrib Man page Source code
plotPrecMassErrorVsScore Man page Source code
plotQValueVsPValue Man page Source code
plotROC Man page Source code
plotRTNorm Man page Source code
plotRTNormSummary Man page Source code
plotScoreDistrib Man page Source code
plotVolcano Man page Source code Source code
plotXYDensity Man page Source code
print.safeQuantAnalysis Source code
purityCorrectTMT Man page Source code
qcPlots Source code
removeOutliers Man page Source code
rollUp Man page Source code
rollUpDT Man page Source code
rtNormalize Man page Source code
safeQuantAnalysis Man page Source code
setFilter Source code
setNbPeptidesPerProtein Man page Source code
setNbSpectraPerProtein Man page Source code
sqImpute Man page Source code
sqNormalize Man page Source code
stripACs Man page Source code
eahrne/SafeQuant documentation built on Dec. 4, 2017, 4:20 p.m.