This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.
|Author||John D. Storey with contributions from Andrew J. Bass, Alan Dabney and David Robinson|
|Date of publication||None|
|Maintainer||John D. Storey <email@example.com>, Andrew J. Bass <firstname.lastname@example.org>|
empPvals: Calculate p-values from a set of observed test statistics and...
hedenfalk: P-values and test-statistics from the Hedenfalk et al. (2001)...
hist.qvalue: Histogram of p-values
lfdr: Estimate local False Discovery Rate (FDR)
pi0est: Proportion of true null p-values
plot.qvalue: Plotting function for q-value object
qvalue: Estimate the q-values for a given set of p-values
summary.qvalue: Display q-value object
write.qvalue: Write results to file