Description Usage Arguments Value Author(s) Examples
This function calculates the F1 score (2*(precision*recall/precision+racall) or 2*TP/(2*TP+FP+FN) given a matrix of pvalues (one for each statistical test used) and a vector of ground truth (DE or nonDE). This function serves as a method evaluation helper.
1  calc.f1score(truth, p, sig = 0.05)

truth 
the ground truth differential
expression vector. It should contain only
zero and nonzero elements, with zero denoting
nondifferentially expressed genes and nonzero,
differentially expressed genes. Such a vector
can be obtained for example by using the

p 
a pvalue matrix whose rows correspond
to each element in the 
sig 
a significance level (0 < 
A named list with two members. The first member is a data frame with the numbers used to calculate the TP/(FP+FN) ratio and the second member is the ratio TP/(FP+FN) for each statistical test.
Panagiotis Moulos
1 2 3 4 5 6 7 8 9  p1 < 0.001*matrix(runif(300),100,3)
p2 < matrix(runif(300),100,3)
p < rbind(p1,p2)
rownames(p) < paste("gene",1:200,sep="_")
colnames(p) < paste("method",1:3,sep="_")
truth < c(rep(1,40),rep(1,40),rep(0,20),rep(1,10),
rep(2,10),rep(0,80))
names(truth) < rownames(p)
f1 < calc.f1score(truth,p)

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