#CalcPValue_Example.R
#Requires R package 'qvalue'

#Requires an (n x p) design matrix 'dataMatrix' and the (n x 10) response matrix 'Y' loaded into memory

#Calculate un-corrected p-values for protein features
#Set 'adrIndex' to the index corresponding to the ADR group of interest
#1 - "neoplasms"
#2 - "bloodAndLymph"
#3 - "immuneSystem"
#4 - "endocrineDisorders"
#5 - "psychDisorders"
#6 - "cardiacDisorders"
#7 - "vascularDisorders"
#8 - "gastroDisorders"
#9 - "hepatoDisorders"
#10 - "renalDisorders"
adrIndex <- 10
proteinPValVect <- vector(length=ncol(dataMatrix))
j <- 0
while(j<ncol(dataMatrix)) {
   j <- j+1
   contMtrx <- matrix(nrow=2,ncol=2)
   contMtrx[1:nrow(contMtrx),1:ncol(contMtrx)] <- 0
   i <- 0
   while(i<nrow(dataMatrix)) {
       i <- i+1
       if ((Y[i,adrIndex]==1)&&(dataMatrix[i,j]==1)) contMtrx[1,1] <- contMtrx[1,1]+1
       if ((Y[i,adrIndex]==1)&&(dataMatrix[i,j]==0)) contMtrx[1,2] <- contMtrx[1,2]+1
       if ((Y[i,adrIndex]==0)&&(dataMatrix[i,j]==1)) contMtrx[2,1] <- contMtrx[2,1]+1
       if ((Y[i,adrIndex]==0)&&(dataMatrix[i,j]==0)) contMtrx[2,2] <- contMtrx[2,2]+1
   }
   pVal <- (fisher.test(x=contMtrx))$p.value
#    zeroValList <- list()
#    oneValList <- list()
#    i <- 0
#    while(i<nrow(dataMatrix)) {
#       i <- i+1
#       if (Y[i,adrIndex]==0) zeroValList <- append(zeroValList,dataMatrix[i,j-1],length(zeroValList))
#       if (Y[i,adrIndex]==1) oneValList <- append(oneValList,dataMatrix[i,j-1],length(oneValList))
#    }
#    zeroValVect <- vector(length=length(zeroValList))
#    oneValVect <- vector(length=length(oneValList))
#    i <- 0;while(i<length(zeroValList)) {i <- i+1;zeroValVect[[i]] <- zeroValList[[i]]}
#    i <- 0;while(i<length(oneValList)) {i <- i+1;oneValVect[[i]] <- oneValList[[i]]}
#    pVal <- (wilcox.test(x=zeroValVect,y=oneValVect))$p.value
    proteinPValVect[[j]] <- pVal
}

#Write out un-corrected p-values
i <- 0
while(i<length(proteinPValVect)) {
   i <- i+1
   print(proteinPValVect[[i]])
}

#Calculate the corresponding q-values
proteinQValVect <- qvalue(p=proteinPValVect)$qvalues

#Write out q-values
i <- 0
while(i<length(proteinQValVect)) {
   i <- i+1
   print(proteinQValVect[[i]])
}