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# Step-down Tippett procedure for strong FWE control
#
# @param P (iter+1) X k matrix of permutation p-values
#
# @return A vector of adjusted p-values
#
# @author Alessandra Cabassi \email{alessandra.cabassi@mail.polimi.it}
FWE.tipp = function(P){
ord = order(P[1,],decreasing=FALSE) # sort the observed p-values in increasing order and store the order
P.ord = P[,ord] # put the columns of matrix P in the new order orde
k = dim(P)[2] # number of tests
p.ris = array(5,dim=c(k,1)) # create vector of adjusted p-values
Pcomb = apply(P.ord,1,min) # combine vectors of p-values with Tippett's comb. fct.
p.ris[1] = p.glob = mean(Pcomb[-1]<=Pcomb[1]) # first adjusted p-value corresponds with the global p-value
if(k>2){ # apply tippett step-down algorithm for p-value adjustement
for(j in 2:(k-1)){
T = apply(P.ord[,j:k],1,min)
p.ris[j] = max(mean(Pcomb[-1]<=Pcomb[1]),p.ris[(j-1)])
}
}
p.ris[k] = max(P.ord[1,k],p.ris[k-1]) # last adjusted p-value
p.ris[ord] = p.ris # put the ajusted p-values in the right order
rownames(p.ris) = colnames(P)
return(p.ris)
}
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