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fdr=function(x,q,method='BH',pi0,lambda=0.5, m0){
#Input checking
stopifnot( is.numeric(x) , is.numeric(q) , any(x<1) , any(x>0) , q<1 , q>0 )
m=length(x)
if(!missing(m0)) stopifnot( is.numeric(m0) , m0<m , m0>=0 )
else if(!missing(m0) & !missing(pi0)) stop("Only m0 or pi0 can be specified.")
else if (method!='Oracle' && !missing(m0) ) stop("m0 can only be specified for the Oracle method.")
else if(missing(m0) & !missing(pi0)) m0=pi0*m
ranks=rank(x)
sorted=sort(x)
# Selecting the propoer procedure
output=switch(method,
'BH'=bh(sorted=sorted,q=q,adjust=TRUE,m=m),
'General Dependency'=bh(sorted=sorted,q=q,m=m,constant=log(m),adjust=TRUE),
'Oracle'=bh(sorted=sorted,q=q,m=m,m0=m0,adjust=TRUE),
'BH Adaptive'=adaptive.bh(sorted=sorted,q=q,m=m),
'ST Adaptive'=adaptive.st(sorted=sorted,q=q,m=m,lambda),
'Two Stage'=two.stage(sorted=sorted,q=q,m=m),
'Multiple Step Down'=multiple.down(sorted=sorted,q=q,m=m),
'Multiple Step Up'=stop("Not implemented yet.") ,#look in file "multiple up (unused).r",
'Smoother'=stop("Not implemented yet.") ,
'Bootstrap'=stop("Not implemented yet."),
'Median ST Adaptive'=stop("Not implemented yet.")
)
#Arranging output
output$Pvals=output$Pvals[ranks,]
output=list(method=method,q=q,Cutoff=output[['Cutoff']],Pvals=output[['Pvals']])
class(output)=c(class(output),'fdr')
return(output)
}
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