ROCplot | R Documentation |
Input an p by d matrix, each column of which contains false positive rates(FPR) computed from each of the d methods and p significance levels and a matrix of corresponding true positive rates(TPR) at the same significance levels. Plot ROC curve for each of the d methods.
ROCplot(fpr,tpr,main, name.method, xlim = c(0,0.2),ylim = c(0.4,1), save = TRUE, name.file = NULL)
fpr |
A matrix of false positive rates for increasing sizes of retrieved significant genes |
tpr |
A vector of corresponding true positive rates at the same significance levels |
main |
a string, title of the figure |
name.method |
a string vector of length d containing names of the d methods |
xlim |
the range of the x axis(FPR), default to c(0,0.2) |
ylim |
the range of the y axis (TPR), default to c(0.4,1) |
save |
a logical value, if |
name.file |
a string giving the name of the png file to save the plot |
The order of the name.method should be the same as that in the fpr and tpr.
Yunting Sun yunting.sun@gmail.com, Nancy R.Zhang nzhang@stanford.edu, Art B.Owen owen@stanford.edu
## Not run: library(sva) library(MASS) library(leapp) data(simdat) model <- cbind(rep(1,60),simdat$g) model0 <- cbind(rep(1,60)) p.raw <- f.pvalue(simdat$data,model,model0) p.oracle <-f.pvalue(simdat$data - simdat$u p.leapp <- leapp(simdat$data,pred.prim = simdat$g, method = "hard")$p p = cbind(p.raw,p.oracle, p.leapp) topk = seq(0,0.5,length.out = 50)*1000 null.set = which(simdat$gamma !=0) fpr= apply(p,2,FindFpr,null.set,topk) tpr= apply(p,2,FindTpr,null.set,topk) ROCplot(fpr,tpr, main = "ROC Comparison", name.method = c("raw","oracle","leapp"), save = FALSE ) ## End(Not run)
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