Nothing
"computeOrirank"<-function(gr1,gr2,logged){
k1=dim(gr1)[2]
k2=dim(gr2)[2]
num.rep=k1*k2
data.rep1=matrix(NA, nrow(gr1),num.rep)
if (logged) {
for (k in 1:k1){
temp=((k-1)*k2+1):(k*k2)
data.rep1[,temp]=gr1[,k]-gr2
}
} else {
for (k in 1:k1) {
temp=((k-1)*k2+1):(k*k2)
data.rep1[,temp]=gr1[,k]/gr2
}
}
temp<-gr1
gr1<-gr2
gr2<-temp
rm(temp)
k1=dim(gr1)[2]
k2=dim(gr2)[2]
num.rep=k1*k2
data.rep2=matrix(NA, nrow(gr1),num.rep)
if (logged) {
for (k in 1:k1){
temp=((k-1)*k2+1):(k*k2)
data.rep2[,temp]=gr1[,k]-gr2
}
} else {
for (k in 1:k1) {
temp=((k-1)*k2+1):(k*k2)
data.rep2[,temp]=gr1[,k]/gr2
}
}
rank.rep1=apply(data.rep1,2,rank) ##rank of genes in the ascending order,
##NA on bottom
rank.rep2=apply(data.rep2,2,rank) ##rank of genes in the ascending order,
## NA on bottom
Orirank<-list(rank.rep1,rank.rep2)
names(Orirank)=c("class1 < class2","class1 > class 2")
Orirank
}
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