betaUniformPvalueSumTest: A meta-analysis P-value summarising a set of hypotheses

In adamsardar/metaDEGth: Combining differential expression P-values in a statistically consistent fashion whilst respecting background signal/noise trends

A meta-analysis P-value summarising a set of hypotheses

Description

A variant of Fisher's method for P-value aggregation, but with a parametrically derived null-hypothesis that reflects the background signal in the data

Usage

betaUniformPvalueSumTest(testPvalues, betaUniformFit, na.rm = TRUE)

## S4 method for signature 'numeric,BetaUniformModel'
betaUniformPvalueSumTest(testPvalues, betaUniformFit, na.rm = TRUE)

## S4 method for signature 'Pvalues,BetaUniformModel'
betaUniformPvalueSumTest(testPvalues, betaUniformFit, na.rm = TRUE)

Arguments

testPvalues	A numerical vector of P-values to be tested.
betaUniformFit	A beta-uniform model of the P-value distribution.
na.rm	Remove NA - default TRUE

Details

Authors in the literature (e.g. Luo et al.) have used a chi-squared test for gene set enrichment with the null-hypothesis that all genes have P-values derived from a pure noise (uniform) distribution. This is typically demonstrably not true and will result in an inflated rate of false positives

Value

combinedPval A single p-value combining the results of multiple hypothesis tests into one

Methods (by class)

• testPvalues = numeric,betaUniformFit = BetaUniformModel: Convert to P-values on the fly

• testPvalues = Pvalues,betaUniformFit = BetaUniformModel: Compute a P-value with the null-hypothesis being that they are drawn randomly from a mixture distribution

References

Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D., & Woolf, P. J. (2009). GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics

https://en.wikipedia.org/wiki/Phase-type_distribution

Sidje RB. Expokit: a software package for computing matrix exponentials. ACM Trans Math Softw. 1998;24: 130–156.

See Also

fishersCombindedProbabilityTest

fitBetaUniformParameters

BioNet::fitBumModel

Other P-value sum tests: fishersPvalueSumTest()

adamsardar/metaDEGth documentation built on Sept. 28, 2022, 10:12 p.m.