### R code from vignette source 'vignettes/MIMOSA/inst/doc/MIMOSA.Rnw'

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### code chunk number 1: sims
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suppressPackageStartupMessages(require(MIMOSA))
require(data.table)
set.seed(100)
effect.sizes.fold<-c(3,3,3)
NN<-c(80000,50000,40000)
Nobs<-rep(NN,3)
Nobs<-100000
pu<-rep(1e-4,3)
ps<-pu*effect.sizes.fold
As<-ps*Nobs
Bs<-(Nobs-As)
A0<-pu*Nobs
B0<-(Nobs-A0)

ANTIGEN.STIM<-c("ENV","GAG","POL")
ANTIGEN.UNSTIM<-c("negctrl","negctrl","negctrl")
CYTOKINE=c("IFNg","IFNg","IFNg")
Ncells<-NN
TCELLSUB=c("CD4")
obs<-100
Nobs<-NN
j<-1
ICS<-do.call(rbind,lapply(seq_along(Nobs),function(i){
sim<-MIMOSA:::simulate2(obs=obs,As=As[j],Bs=Bs[j],A0=A0[j],B0=B0[j],NS=NN[i],N0=NN[i],w2=0.5,alternative="greater")
stim<-sim[,c("Ns","ns")]
unstim<-sim[,c("Nu","nu")]
colnames(stim)<-c("NSUB","CYTNUM")
colnames(unstim)<-c("NSUB","CYTNUM")
df<-rbind(stim,unstim)
data.frame(df,ANTIGEN=gl(2,obs,labels=c(ANTIGEN.STIM[i],ANTIGEN.UNSTIM[i])),CYTOKINE=CYTOKINE[i],TCELLSUBSET=TCELLSUB[1],UID=rep(gl(obs,1),2))
}))
ICS<-cbind(ICS,Ntot=factor(ICS$NSUB+ICS$CYTNUM))
ICS$Stim<-factor(ICS$Ntot,labels=c("ENV","GAG","POL"))
ggplot(ICS)+geom_histogram(aes(x=CYTNUM,fill=(ANTIGEN%in%"negctrl")),alpha=0.5,position="identity")+facet_wrap(~Stim)+scale_fill_discrete("stimulation",labels=c("negctrl","Stim"))


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### code chunk number 2: loaddata
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require(MIMOSA)
head(ICS)


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### code chunk number 3: Eset
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E<-ConstructMIMOSAExpressionSet(ICS,
                                reference=ANTIGEN%in%"negctrl",
                                measure.columns=c("CYTNUM","NSUB"),
                                other.annotations=c("CYTOKINE","TCELLSUBSET","ANTIGEN","UID","Ntot"),
                                default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET+Ntot,
                                .variables=.(TCELLSUBSET,CYTOKINE,UID,Ntot),
                                featureCols=1,ref.append.replace="_REF")