qvalue v2.4.2

by John D Storey

Q-value estimation for false discovery rate control

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.

Functions in qvalue

Name Description
plot.qvalue Plotting function for q-value object
lfdr Estimate local False Discovery Rate (FDR)
pi0est Proportion of true null p-values
hist.qvalue Histogram of p-values
hedenfalk P-values and test-statistics from the Hedenfalk et al. (2001) gene expression dataset
qvalue Estimate the q-values for a given set of p-values
write.qvalue Write results to file
summary.qvalue Display q-value object
empPvals Calculate p-values from a set of observed test statistics and simulated null test statistics
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Details

Type Package
Date 2015-03-24
biocViews MultipleComparisons
VignetteBuilder knitr
URL http://github.com/jdstorey/qvalue
License LGPL
RoxygenNote 5.0.1

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