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Luke Zappia authored
Store gene parameters in data.frame rather than separate vectors. Forces them to be same length and allows more independence between gene parameters and nGenes. Checking for differences between the number of gene parameters and nGenes, and sampling if necessary, is now done in `lun2Simulate` rather than `validObject`. The same is true for nCells and lib.sizes.
Luke Zappia authoredStore gene parameters in data.frame rather than separate vectors. Forces them to be same length and allows more independence between gene parameters and nGenes. Checking for differences between the number of gene parameters and nGenes, and sampling if necessary, is now done in `lun2Simulate` rather than `validObject`. The same is true for nCells and lib.sizes.
NAMESPACE 2.67 KiB
# Generated by roxygen2: do not edit by hand
S3method(lun2Estimate,SCESet)
S3method(lun2Estimate,matrix)
S3method(lunEstimate,SCESet)
S3method(lunEstimate,matrix)
S3method(scDDEstimate,SCESet)
S3method(scDDEstimate,matrix)
S3method(simpleEstimate,SCESet)
S3method(simpleEstimate,matrix)
S3method(splatEstimate,SCESet)
S3method(splatEstimate,matrix)
export(addGeneLengths)
export(compareSCESets)
export(diffSCESets)
export(getParam)
export(getParams)
export(listSims)
export(lun2Estimate)
export(lun2Simulate)
export(lunEstimate)
export(lunSimulate)
export(newLun2Params)
export(newLunParams)
export(newSCDDParams)
export(newSimpleParams)
export(newSplatParams)
export(scDDEstimate)
export(scDDSimulate)
export(setParam)
export(setParams)
export(simpleEstimate)
export(simpleSimulate)
export(splatEstimate)
export(splatSimulate)
export(splatSimulateGroups)
export(splatSimulatePaths)
export(splatSimulateSingle)
exportClasses(Lun2Params)
exportClasses(LunParams)
exportClasses(SCDDParams)
exportClasses(SimpleParams)
exportClasses(SplatParams)
importFrom(Biobase,"fData<-")
importFrom(Biobase,"pData<-")
importFrom(Biobase,assayData)
importFrom(Biobase,fData)
importFrom(Biobase,pData)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(checkmate,checkCharacter)
importFrom(checkmate,checkClass)
importFrom(checkmate,checkDataFrame)
importFrom(checkmate,checkFactor)
importFrom(checkmate,checkFlag)
importFrom(checkmate,checkInt)
importFrom(checkmate,checkIntegerish)
importFrom(checkmate,checkNumber)
importFrom(checkmate,checkNumeric)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(locfit,locfit)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(methods,validObject)
importFrom(scater,"cpm<-")
importFrom(scater,"set_exprs<-")
importFrom(scater,counts)
importFrom(scater,get_exprs)
importFrom(scater,newSCESet)
importFrom(stats,dnbinom)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,nls)
importFrom(stats,rbinom)
importFrom(stats,rchisq)
importFrom(stats,rgamma)
importFrom(stats,rlnorm)
importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
importFrom(utils,head)