# Data analysis for cell-based functional assays

## Documentation for package ‘prada’ version 1.63.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

$.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
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-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-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-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-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
applyGate-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-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
barploterrbar | Barplot with error bars.
cframe | A sample cytoFrame object - German Cancer Research Center Heidelberg -
colnames-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-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
colnames<--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<--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
description-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<--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-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-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<--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
fitNorm2 | Fit bivariate normal distribution.
gate | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
gate-class | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
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<- | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
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
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
getAlphaNumeric | Convert from plate coordinates to alphanumeric notation.
getPradaPar | Set and query global parameters for functions in the prada package
hist-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-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
killProgress | A simple tcltk progress window
length-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
length-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
lines-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
names-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
names-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
names<--method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
names<--method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
ncol-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-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
pData-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
phenoData-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
phenoData<--method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
plot-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-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
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
removeCensored | Remove rows that contain censored data
removeCensored-method | Remove rows that contain censored data
setPradaPars | Set and query global parameters for functions in the prada package
show-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-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
show-method | 'gate': a class for subsetting flow-cytometry data by defining regions in two-dimesional projections of the data
show-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
split-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
threePanelPlot | Visualize cytometry data
thresholds | Discretize a two-dimensional data space into quadrants by applying thresholds
touchFCS | Check for FCS files
updateProgress | A simple tcltk progress window
vpLocation | Absolute location of current viewport
[-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
[-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
[[-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[[-method | 'gateSet': a class for subsetting flow-cytometry data by defining multiple regions in two-dimesional projections of the data
[[<--method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay