R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 13 found.
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ITNQASTUDY (Package: QUALIFIER) : The example QA data included in the package

Once 'ITNQASTUDY' is loaded by data function, an environment 'db' is generated, which contains:

● Data Source: BioConductor
● Keywords: data
● Alias: ITNQASTUDY, db, qaCheckList, tubesevents
● 0 images

QUALIFIER-package (Package: QUALIFIER) : QUALIFIER: A package that provides automated flow data quality assessment

The package provide two important methods:qaCheck and plot, which allows users to use formula as a general and flexible way to specify the tubes,channels,statistics and gated populations to perform differnt QA tasks.

● Data Source: BioConductor
● Keywords: package
● Alias: QUALIFIER, QUALIFIER-package
● 0 images

getQAStats (Package: QUALIFIER) : Get statistics from gated data for QA check.

getQAStats calculates and extract statistics of each gated cell population in the gating hierarchies generated by flowWorkspace package.

● Data Source: BioConductor
● Keywords: methods
● Alias: getQAStats, getQAStats,GatingHierarchy-method, getQAStats,GatingSet-method, getQAStats,GatingSetList-method, getQAStats,environment-method, getQAStats-methods
● 0 images

initDB (Package: QUALIFIER) : Initializes the data environment

Initializes and prepares the data environment for storing the QA data

● Data Source: BioConductor
● Keywords:
● Alias: initDB
● 0 images

proportion.outliers.robust (Package: QUALIFIER) : outliers detection functions

Distribution based outlier detection functions.

● Data Source: BioConductor
● Keywords: functions
● Alias: outlier.cutoff, outlier.norm, outlier.t, outlierFunctions, proportion.outliers.mle, proportion.outliers.robust, qoutlier, rlm
● 0 images

plot-methods (Package: QUALIFIER) : plot the statistics for a particular cell population of a group of samples

plot the statistics for a particular cell population of a group of samples,this method is usually called after qaCheck to visualize the QA results.

● Data Source: BioConductor
● Keywords: methods
● Alias: plot, plot,qaTask,ANY-method, plot,qaTask-method, plot-methods
● 0 images

queryStats (Package: QUALIFIER) : Perform the quality assessment for the qaTask object

queryStats method queries stats entries from db by qaTask object and formula

● Data Source: BioConductor
● Keywords: methods
● Alias: clearCheck, qaCheck, qaCheck,qaTask-method, qaCheck-methods, queryStats, queryStats,qaTask-method
● 0 images

qaPreprocess (Package: QUALIFIER) : Preprocessing for QA check

A convenient wrapper that does saveToDB, getQAStats in one call

● Data Source: BioConductor
● Keywords:
● Alias: qaPreprocess
● 0 images

qaReport (Package: QUALIFIER) : create quality assessment report

create quality assessment report in HTML format, which contains the annotated svg summary plot for each QA task.

● Data Source: BioConductor
● Keywords: methods
● Alias: qaReport, qaReport,list-method, qaReport,qaTask-method, qaReport-methods
● 0 images

qaTask-class (Package: QUALIFIER) : a class for storing important information of flow cytometry data quality assessment task

This class stores the meta information, the name of gated cell population associated with the QA task and the formula describing how the QA task is performed.

● Data Source: BioConductor
● Keywords: classes
● Alias: description,qaTask, formula,qaTask, getData,qaTask, getName,qaTask, getPop,qaTask, highlight, highlight,qaTask-method, highlight<-, highlight<-,qaTask,character-method, htmlReport, htmlReport,qaTask-method, htmlReport<-, htmlReport<-,qaTask,logical-method, plotType,qaTask, qaID,qaTask, qaLevel,qaTask, qaTask, qaTask-class, qpar, qpar,qaTask-method, qpar<-, qpar<-,qaTask,list-method, rFunc, rFunc,qaTask-method, rFunc<-, rFunc<-,qaTask,ANY-method, rFunc<-,qaTask-method, scatterPar, scatterPar,qaTask-method, scatterPar<-, scatterPar<-,qaTask,list-method, show,qaTask
● 0 images