# Qualitiy control for flow cytometry

## Documentation for package ‘flowQ’ version 1.6.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

flowQ-package | Quality control for flow cytometry
aggregatorList | Class "aggregatorList"
aggregatorList-class | Class "aggregatorList"
binaryAggregator | Class "binaryAggregator"
binaryAggregator-class | Class "binaryAggregator"
discreteAggregator | Class "discreteAggregator"
discreteAggregator-class | Class "discreteAggregator"
evaluateProcess | Evaluate QA processes
factorAggregator | Class "factorAggregator"
factorAggregator-class | Class "factorAggregator"
flowQ | Quality control for flow cytometry
initialize,aggregatorList-method | Class "aggregatorList"
initialize,qaGraph-method | Class "qaGraph"
initialize,qaGraphList-method | Class "qaGraphList"
initialize,qaProcess-method | Abstraction of the results of a QA process
initialize,qaProcessFrame-method | Class "qaProcessFrame"
locateDuplicatedParameters | Locate Duplicated Parameters
names,qaGraph-method | Class "qaGraph"
normalizeSets | Locate Duplicated Parameters
numericAggregator | Class "numericAggregator"
numericAggregator-class | Class "numericAggregator"
outlier-class | Virtual Class "outlier"
outlierResult-class | Class "outlierResult"
outliers | ~~ Methods for Function outliers in Package '.GlobalEnv' ~~
outliers,flowSet-method | ~~ Methods for Function outliers in Package '.GlobalEnv' ~~
outliers-methods | ~~ Methods for Function outliers in Package '.GlobalEnv' ~~
preProcessFlowList | Preprocess a list of flowSets to add empty flowFrames for patients in which certain aliquots are missing
qaAggregator | Abstraction of the possible outcomes of a QA process
qaAggregator-class | Abstraction of the possible outcomes of a QA process
qaGraph | Class "qaGraph"
qaGraph-class | Class "qaGraph"
qaGraphList | Class "qaGraphList"
qaGraphList-class | Class "qaGraphList"
qaProcess | Abstraction of the results of a QA process
qaProcess-class | Abstraction of the results of a QA process
qaProcess.2DStatsPlot | Creates a QA process for 2D summary statistic comparisons across multiple samples
qaProcess.BoundaryPlot | Creates a QA process for comparison of the percentage of boundary events for the specified parameters across multiple samples
qaProcess.cellnumber | Create QA process of type 'cellnumber'
qaProcess.DensityPlot | Creates a QA process for comparisons of density plots across multiple samples
qaProcess.ECDFPlot | Creates a QA process for comparisons of ECDF's across multiple samples
qaProcess.KLDistPlot | Creates a QA process for comparisons of KL Distances across multiple samples
qaProcess.marginevents | Create QA process of type 'marginevents'
qaProcess.timeflow | Create QA process of type 'timeflow'
qaProcess.timeline | Create QA process of type 'timeline'
qaProcessFrame | Class "qaProcessFrame"
qaProcessFrame-class | Class "qaProcessFrame"
qaProcessSummary | Class "qaProcessSummary"
qaProcessSummary-class | Class "qaProcessSummary"
qaReport | Create HTML report using one or several QA process function(s)
qData | Data for demonstrating QA processes that compares dye parameters from each patient across multiple aliquots
rangeAggregator | Class "rangeAggregator"
rangeAggregator-class | Class "rangeAggregator"
show,aggregatorList-method | Class "aggregatorList"
show,binaryAggregator-method | Class "binaryAggregator"
show,discreteAggregator-method | Class "discreteAggregator"
show,factorAggregator-method | Class "factorAggregator"
show,numericAggregator-method | Class "numericAggregator"
show,qaGraph-method | Class "qaGraph"
show,qaGraphList-method | Class "qaGraphList"
show,qaProcess-method | Abstraction of the results of a QA process
show,qaProcessFrame-method | Class "qaProcessFrame"
show,qaProcessSummary-method | Class "qaProcessSummary"
show,rangeAggregator-method | Class "rangeAggregator"
show,stringAggregator-method | Class "stringAggregator"
stringAggregator | Class "stringAggregator"
stringAggregator-class | Class "stringAggregator"
txtFormatQAObject | Formats results contained in QA process objects into a data frame with appropriate row and column names
validProcess | Validate a QAProcess object
writeLines,binaryAggregator,file,missing,missing-method | Class "binaryAggregator"
writeLines,data.frame,file,missing,missing-method | Create HTML report for (lists of) qaProcess objects
writeLines,discreteAggregator,file,missing,missing-method | Class "discreteAggregator"
writeLines,factorAggregator,file,missing,missing-method | Class "factorAggregator"
writeLines,numericAggregator,file,missing,missing-method | Class "numericAggregator"
writeLines,qaProcessSummary,file,missing,missing-method | Class "qaProcessSummary"
writeLines,rangeAggregator,file,missing,missing-method | Class "rangeAggregator"
writeLines,stringAggregator,file,missing,missing-method | Class "stringAggregator"
writeQAReport | Create HTML report for (lists of) qaProcess objects
writeQATextReport | Create tab delimited text files for (lists of) qaProcess objects