# Data analysis for cell-based functional assays

## Documentation for package `prada' version 1.10.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E F G H I K L N P R S T U V misc

$.cytoFrame | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy

## -- A --

analysePlate | Apply a statistic to the data from each well in a plate
appendGates | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
appendGates, gateSet_method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
appendGates,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
appendGates,gateSet-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
applyGate | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
applyGate,cytoFrame,character-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
applyGate,cytoFrame,gate-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
applyGate,cytoFrame,gateSet-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
applyGate,cytoFrame,logical-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
applyGate,cytoFrame,numeric-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
applyGate,matrix,gate-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
applyGate,matrix,gateSet-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
as.all | Coercion without introduction of NAs
as.gateSet | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
as.gateSet,gate-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data

## -- B --

barploterrbar | Barplot with error bars.

## -- C --

cframe | A sample cytoFrame object - German Cancer Research Center Heidelberg -
colnames,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
colnames,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
colnames<-,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
colnames<-,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
combineFrames | Combine the cytoFrames within a cytoSet according to some grouping factor
combineGates | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
csApply | Apply a function over the intensities in a cytoSet
cset | A sample cytoSet object - German Cancer Research Center Heidelberg -
cytoFrame | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
cytoFrame-class | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
cytoSet | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
cytoSet-class | 'cytoSet': a class for storing raw data from a quantitative cell-based assay

## -- D --

ddCt | Apply the ddCt method for a given data set
ddCtSet-class | Class for storage of relative rtPCR results
description,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
description<-,cytoFrame,character-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
devDims | Device Dimensions for plate plots
devRes | Resolution of current plotting device
drawGate | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
drawGate,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
drawGate,matrix-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy

## -- E --

eListWrite | Write the eList
exprs,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
exprs,ddCtSet-method | Class for storage of relative rtPCR results
exprs<-,cytoFrame,matrix-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
exprs<-,ddCtSet,matrix-method | Class for storage of relative rtPCR results

## -- F --

fitNorm2 | Fit bivariate normal distribution.

## -- G --

gate | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
gate,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
gate-class | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
gate<-,cytoFrame,gate-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
gate<-,cytoFrame,gateSet-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
gateSet | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
gateSet-class | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
getPradaPar | Set and query global parameters for functions in the prada package

## -- H --

hist,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
hist,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay

## -- I --

initialize,ddCtSet-method | Class for storage of relative rtPCR results

## -- K --

killProgress | A simple tcltk progress window

## -- L --

length,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
length,gateSet-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
lines,gate-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data

## -- N --

names,gate-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
names,gateSet-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
names<-,gate-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
names<-,gateSet-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
ncol,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
nrow,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy

## -- P --

pData,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
phenoData,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
phenoData<-,cytoSet,phenoData-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
plot,cytoFrame,missing-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
plot,cytoSet,missing-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
plotNorm2 | Plot fitted bivariate normal distribution.
plotPlate | Plot a well statistic for microtiter plates.
progress | A simple tcltk progress window

## -- R --

read.fcs | Read an FCS file
readCytoSet | Create a cytoSet object from one or more FCS 3.0 files
readFCS | Read an FCS file
readFCSdata | Auxiliary functions for readFCS
readFCSgetPar | Auxiliary functions for readFCS
readFCSheader | Auxiliary functions for readFCS
readFCStext | Auxiliary functions for readFCS
readSDM | Read an SDM file
removeCensored | Remove rows that contain censored data
removeCensored,cytoFrame-method | Remove rows that contain censored data
removeCensored,data.frame-method | Remove rows that contain censored data
removeCensored,matrix-method | Remove rows that contain censored data

## -- S --

setPradaPars | Set and query global parameters for functions in the prada package
show,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
show,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
show,gate-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
show,gateSet-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data

## -- T --

threePanelPlot | Visualize cytometry data
thresholds | Discretize a two-dimensional data space into quadrants by applying thresholds
touchFCS | Check for FCS files

## -- U --

updateProgress | A simple tcltk progress window

## -- V --

vpLocation | Absolute location of current viewport

## -- misc --

[,cytoFrame-method | 'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy
[,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[,gateSet-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
[[,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[[,gateSet-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
[[<-,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay