betaUniformScore: For each P-value, compute the log likelihood ratio of...

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

For each P-value, compute the log likelihood ratio of originating from signal or noise component

Description

Relative to some false discovery threshold, compute the relative ratio of probabilities and then take the natural logarithm. This function is somewhat analagous to BioNet::scoreNodes

Usage

betaUniformScore(x, betaUniformFit = NULL, FDR = 0.05)

## S4 method for signature 'Pvalues,BetaUniformModel,ScalarNumeric'
betaUniformScore(x, betaUniformFit = NULL, FDR = 0.05)

## S4 method for signature 'igraph,ANY,ANY'
betaUniformScore(x, betaUniformFit = NULL, FDR = 0.05)

## S4 method for signature 'numeric,ANY,ANY'
betaUniformScore(x, betaUniformFit = NULL, FDR = 0.05)

## S4 method for signature 'ANY,ANY,numeric'
betaUniformScore(x, betaUniformFit = NULL, FDR = 0.05)

## S4 method for signature 'BetaUniformModel,missing,ANY'
betaUniformScore(x, betaUniformFit = NULL, FDR = 0.05)

## S4 method for signature 'Pvalues,'NULL',ANY'
betaUniformScore(x, betaUniformFit = NULL, FDR = 0.05)

## S4 method for signature 'ANY,bum,ANY'
betaUniformScore(x, betaUniformFit = NULL, FDR = 0.05)

Arguments

x	data
betaUniformFit	(optional) A beta-uniform model of the P-value distribution. Set to NULL to autofit on the fly.
FDR	The tolerable fraction of false positives within the set of positive scoring values. See Morris & Pounds (2003)

Value

betaUniformScores A vector of P-Value scores

Functions

• betaUniformScore,Pvalues,BetaUniformModel,ScalarNumeric-method: Score P-values against an explicit beta-uniform model object

• betaUniformScore,igraph,ANY,ANY-method: Score nodes in an igraph; there must be a 'pValue'-like attribute (pVal, p.value etc.)

• betaUniformScore,numeric,ANY,ANY-method: Score nodes from numeric object

• betaUniformScore,ANY,ANY,numeric-method: Score nodes default

• betaUniformScore,BetaUniformModel,missing,ANY-method: Score p-values from a BetaUniformModel object against inself

• betaUniformScore,Pvalues,NULL,ANY-method: Score P-values against a Beta-uniform model fit on the fly.

• betaUniformScore,ANY,bum,ANY-method: Score P-values against a beta-uniform model S3 object from BioNet

References

Pounds, S., & Morris, S. W. (2003). Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics

Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T. Identifying functional modules in protein-protein interaction networks: An integrated exact approach. Bioinformatics. 2008

See Also

fitBetaUniformParameters BioNet::scoreNodes

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