Nothing
tanova<-function(data, f1, f2, tp, B=100, FDR=0.05,robustify=FALSE, equal.size=FALSE, qt=-1, longitudinal=TRUE, test.type=0,eb=FALSE,df=0){
type<-test.type
if (length(tp)==1){
if (type==0){
return(gene.classifier1(data,f1,f2,B=B,FDR=FDR,robustify=robustify, equal.size=equal.size,qt=qt,eb=eb))
}
if (type!=0){
o<-NANOVA.test(data=data,f1=f1,f2=f2,robustify=robustify, equal.size=equal.size, type=type,B=B,eb=eb)
fdr<-fdr.table(o)
c<-sig.number(fdr, FDR=FDR, qt=qt)
s<-o$gene.order[1:c]
p<-o$pvalue
dt<-o$delta
return(list(genes=s, pvalue=p[s],delta=dt[s],obj=o))
}
}
if (longitudinal==TRUE & length(tp)>1){
temp<-data.form(data=data,f1=f1,f2=f2,tp=tp)
d<-temp$d
fc1<-temp$fc1
fc2<-temp$fc2
if (type==0){
return(gene.classifier2(data=d,f1=fc1,f2=fc2,B=B,FDR=FDR,robustify=robustify, equal.size=equal.size,time.course=length(unique(tp)),qt=qt,eb=eb,df=df))
}
if (type!=0){
o<-NANOVA.test2(data=d,f1=fc1,f2=fc2,time.course=length(unique(tp)),robustify=robustify, equal.size=equal.size, type=type,B=B,eb=eb,df=df)
fdr<-fdr.table(o)
c<-sig.number(fdr, FDR=FDR, qt=qt)
s<-o$gene.order[1:c]
p<-o$pvalue
dt<-o$delta
a<-proj.dir(data=d,f1=fc1,f2=fc2,time.course=length(unique(tp)),type=type,df=df)
return(list(genes=s, pvalue=p[s],delta=dt[s],a=a[s,],obj=o,dir=a))
}
}
if (longitudinal==FALSE & length(tp)>1){
if (type==0){
return (gene.classifier3(data=data,f1=f1,f2=f2,tp=tp,B=B,FDR=FDR,qt=qt,robustify=robustify,eb=eb))
}
if (type!=0){
o<-NANOVA.test3(data=data,f1=f1,f2=f2,tp=tp,type=type,B=B,robustify=robustify,eb=eb)
fdr<-fdr.table(o)
c<-sig.number(fdr, FDR=FDR, qt=qt)
s<-o$gene.order[1:c]
p<-o$pvalue
dt<-o$delta
tm<-0
if (robustify==TRUE){
tm<-0.2
}
a<-proj.dir2(data=data,f1=f1,f2=f2,tp=tp,type=type,trim=tm)
return(list(genes=s, pvalue=p[s],delta=dt[s],a=a[s,],obj=o,dir=a))
}
}
}
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