Data analysis for cell-based functional assays


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Documentation for package `prada' version 1.3.1

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$.cytoFrame 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy
analysePlate Apply a statistic to the data from each well in a plate
as.all Coercion without introduction of NAs
barploterrbar Barplot with error bars.
colnames,cytoFrame-method 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or 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, for example from a FACS run or 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
csApply Apply a function over the intensities in a cytoSet
cytoFrame-class 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy
cytoSet-class 'cytoSet': a class for storing raw data from a quantitative cell-based assay
ddCt Apply the ddCt method for a given data set
description,cytoFrame-method 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy
description<-,cytoFrame,character-method 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy
eListWrite Write the eList
exprs,cytoFrame-method 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy
exprs<-,cytoFrame,matrix-method 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy
fitNorm2 Fit bivariate normal distribution.
getPradaPar Set and query global parameters for functions in the prada package
histStack Stacked histogram
length,cytoSet-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay
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
plotNorm2 Plot fitted bivariate normal distribution.
plotPlate Plot a well statistic in false color representation.
readCytoSet Create a cytoSet object from one or more FCS 3.0 files
readFCS Read an FCS 3.0 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
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, for example from a FACS run or from automated microscopy
show,cytoSet-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay
thresholds Discretize a two-dimensional data space into quadrants by applying thresholds
[,cytoFrame-method 'cytoFrame': a class for storing observed quantitative properties from a population of cells, for example from a FACS run or from automated microscopy
[,cytoSet-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[[,cytoSet-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[[<-,cytoSet-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay