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  • Luke Zappia's avatar
    012355a3
    Modify Lun2Params to use data.frame · 012355a3
    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.
    012355a3
    History
    Modify Lun2Params to use data.frame
    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.
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)