errDisc: Obtains estimates of the following quantities: expected...

In leekgroup/Set: Decision-theoretic approach to gene-set analysis

Description

This function inputs a list of non-overlapping sets (atoms) and a vector of estimated gene-level posterior probabilities of differential expression, and outputs a matrix with estimates of the following quantities: expected number of false discoveries (EFD), the expected number of missed discoveries (EFD), the expected fraction of false discoveries (EFDR), and the expected fraction of missed discoveries (EMDR) for the given atoms.

Usage

errDisc(atoms, post.prob.genes)

Arguments

atoms	A list of non-overlapping sets (atoms).
post.prob.genes	Vector of the estimated gene-level probabilities of differential expression (output from postProb.)

Value

Matrix with the estimated EFD, EMD, EFDR, and EMDR for each atom in atoms as columns.

Author(s)

Simina M. Boca

References

Boca S.M., H. Corrada Bravo, B. Caffo, J.T. Leek, and G. Parmigiani (2010): A decision-theory approach to interpretable set analysis for high-dimensional data, JHU Biostat Working Paper 211, http://www.bepress.com/jhubiostat/paper211/

See Also

postProb

Examples

##first obtain estimates of the gene-level posterior probabilities
data(GenderStats)
data(ChromSets)

gene.stat <- (gene.stat - mean(gene.stat))/sd(gene.stat)
set.seed(70790707)
post.prob.genes <- postProb(gene.stat, null = rnorm(20 * length(gene.stat),
+ 0, 1), K = length(gene.stat))

##now run errDisc function
EFD.EMD.res <- errDisc(sets, post.prob.genes)
head(EFD.EMD.res)

leekgroup/Set documentation built on May 20, 2019, 11:30 p.m.