R/AllGenerics.R

In plateCore: Statistical tools and data structures for plate-based flow cytometry

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## Filename: AllGenerics.R
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## Author: straine
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## Data: Apr 27, 2007
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## Description:
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setGeneric("flowPlate", function(data,wellAnnotation,plateName,...) standardGeneric("flowPlate"))

setGeneric("fixAutoFl", function(fp,fsc="FSC.A",chanCols,unstain=NULL,...) standardGeneric("fixAutoFl"))

setGeneric("setControlGates", function(data,gateType="Negative.Control",threshType="MAD",numMads=5,isoquantile=.995,...) standardGeneric("setControlGates"))

setGeneric("plateSet", function(fp,...) standardGeneric("plateSet"))

setGeneric("wellAnnotation", function(fp,...) standardGeneric("wellAnnotation"))

setGeneric("applyControlGates", function(data,gateType="Negative.Control",...) standardGeneric("applyControlGates"))

setGeneric("summaryStats", function(data,Events="Percentage",...) standardGeneric("summaryStats"))

setGeneric("getGroups", function(data,type="Negative.Control",chan,...) standardGeneric("getGroups"))

setGeneric("fpbind", function(p1,p2,...) standardGeneric("fpbind"))

setGeneric("plotPlate", function(fp,x=NA,method="median",main,col,values,
				width=1,na.action="zero",...) standardGeneric("plotPlate"))

setGeneric("gutterPlot", function(fp,chans=c("FSC-H","SSC-H","FL1-H","FL2-H","FL3-H","FL4-H"),...) standardGeneric("gutterPlot"))

setGeneric("mfiPlot", function(fp,thresh=2,Sample.Type="Test",Events="Percentage",...) standardGeneric("mfiPlot"))

setGeneric("setGate",function(fp,chan,wells,newGate,type="Negative.Control.Gate",...) standardGeneric("setGate"))

setGeneric("adjustGateLog10",function(fp,wells,chan,xlim,ylim,
				fsc="FSC.A",asFact="Well.Id",numEvents=250,type="Negative.Control.Gate",...) standardGeneric("adjustGateLog10"))
			
setGeneric("xyplot", function(x, data, ...) standardGeneric("xyplot"))

setGeneric("densityplot", function(x, data, ...) standardGeneric("densityplot"))