Nothing
## ---- results="hide", message=FALSE--------------------------------------
library(penalized)
data(nki70)
## ----warning=FALSE-------------------------------------------------------
library(survival)
set.seed(21983)
w<-100 # number of random permutations
pvalues <- matrix(nr=w,nc=70)
survobj <- Surv(time=nki70$time, event=nki70$event)
#compute the 70 p-values for each random permutation
for(j in 1:w){
if(j==1){
permdata <- nki70 #original data
}
else{
permdata <- nki70[sample(nrow(nki70)),] #randomly shuffle the rows
}
for (i in 1:70) {
form <- as.formula(paste("survobj ~ ", names(nki70)[i+7] ))
coxobj <- coxph(form, data=permdata)
sumcoxobj <- summary(coxobj)
pvalues[j,i] <- sumcoxobj$coefficients[,5]
}
}
## ------------------------------------------------------------------------
sum(pvalues[1,]<0.03)
## ------------------------------------------------------------------------
library(confSAM)
confSAM(p=pvalues[1,], PM=pvalues, cutoff=0.03, alpha=0.1, method="simple")[3]
## ------------------------------------------------------------------------
confSAM(p=pvalues[1,], PM=pvalues, cutoff=0.03, alpha=0.1, method="simple")
## ------------------------------------------------------------------------
confSAM(p=pvalues[1,], PM=pvalues, cutoff=0.03, alpha=0.1, method="full")
## ------------------------------------------------------------------------
#simple method
confSAM(p=pvalues[1,], PM=pvalues, cutoff=0.2, alpha=0.1, method="simple")
#approximation method
confSAM(p=pvalues[1,], PM=pvalues, cutoff=0.2, alpha=0.1, method="approx", ncombs=1000)[3]
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