Data analysis for cell-based functional assays


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Documentation for package ‘prada’ version 1.18.0

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A B C D E F G H 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 --

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 --

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<-,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

-- 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

-- 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,AnnotatedDataFrame-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
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
split,cytoSet,ANY,ANY-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay
split,cytoSet,ANY-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay
split,cytoSet-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay

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