Statistical tools and data structures for plate-based flow cytometry


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Documentation for package ‘plateCore’ version 1.4.0

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plateCore-package plateCore: A Bioconductor package for high throughput analysis of flow cytometry data
%on% Methods for Function %on% in Package 'plateCore'
%on%,ANY,flowPlate-method Methods for Function %on% in Package 'plateCore'
%on%-methods Methods for Function %on% in Package 'plateCore'
applyControlGates Apply control gates to a flowPlate
applyControlGates,flowPlate-method Apply control gates to a flowPlate
applyControlGates-methods Apply control gates to a flowPlate
compensate Compensate a flowPlate to correct for the effects of spillover.
compensate,flowPlate,ANY-method Compensate a flowPlate to correct for the effects of spillover.
compensate-method Compensate a flowPlate to correct for the effects of spillover.
compensationSet Sample Compensation Data Set
densityplot One-dimensional density plots for flowPlates
densityplot,formula,flowPlate,ANY,ANY,ANY,missing-method One-dimensional density plots for flowPlates
densityplot,formula,flowPlate-method One-dimensional density plots for flowPlates
densityplot-method One-dimensional density plots for flowPlates
fixAutoFl Correct for the effects of cell size (FSC) on autofluorescence
fixAutoFl,flowPlate-method Correct for the effects of cell size (FSC) on autofluorescence
fixAutoFl-method Correct for the effects of cell size (FSC) on autofluorescence
flowPlate Create a flowPlate
flowPlate,flowSet-method Create a flowPlate
flowPlate-class The flowPlate class.
flowPlate-method Create a flowPlate
fpbind Merge multiple flowPlates into a single virtual flowPlate
fpbind,flowPlate,flowPlate-method Merge multiple flowPlates into a single virtual flowPlate
fpbind-method Merge multiple flowPlates into a single virtual flowPlate
getGroups Retrieve Negative control groups from a flowPlate
getGroups,flowPlate-method Retrieve Negative control groups from a flowPlate
getGroups-method Retrieve Negative control groups from a flowPlate
gutterPlot gutterPlot
gutterPlot,flowPlate-method gutterPlot
gutterPlot-method gutterPlot
mfiPlot mfiPlot
mfiPlot,flowPlate-method mfiPlot
mfiPlot-method mfiPlot
panel.densityplot.flowPlate Lattice-flowViz style panel function for flowPlate densityplot.
panel.xyplot.flowPlate Lattice-flowViz style panel function for flowPlate xyplot.
pbmcPlate pbmcPlate Data Set
phenoData,flowPlate-method Create a flowPlate
plateCore plateCore: A Bioconductor package for high throughput analysis of flow cytometry data
plateSet Get the flowSet from a flowPlate object
plateSet,flowPlate-method Get the flowSet from a flowPlate object
plateSet-method Get the flowSet from a flowPlate object
plotPlate plotPlate
plotPlate,flowPlate-method plotPlate
plotPlate-method plotPlate
prepanel.densityplot.flowPlate Lattice-flowViz style panel function for flowPlate densityplot.
prepanel.xyplot.flowPlate Lattice-flowViz style panel function for flowPlate xyplot.
sampleNames,flowPlate-method Create a flowPlate
setControlGates Create control gates for a flowPlate
setControlGates,flowPlate-method Create control gates for a flowPlate
setControlGates-method Create control gates for a flowPlate
Subset Subset
Subset,flowPlate,ANY-method Subset
Subset,flowPlate-method Subset
Subset-method Subset
summaryStats Compute summary statistics on a flowPlate
summaryStats,flowPlate-method Compute summary statistics on a flowPlate
summaryStats-method Compute summary statistics on a flowPlate
wellAnnotation Retrieve a data.frame describing the content of a flowPlate
wellAnnotation,flowPlate-method Retrieve a data.frame describing the content of a flowPlate
wellAnnotation-method Retrieve a data.frame describing the content of a flowPlate
xyplot Scatter plots (dotplots) for flowPlates.
xyplot,formula,flowPlate-method Scatter plots (dotplots) for flowPlates.
xyplot-method Scatter plots (dotplots) for flowPlates.
[,flowPlate,ANY-method The flowPlate class.
[[,flowPlate,ANY-method The flowPlate class.