CausalR (version 1.4.3)

CalculateSignificanceUsingQuarticAlgorithm: calculate significance using the quartic algorithm

Description

Computes the significance of a given hypothesis. For a detailed description of the algorithm see Causal reasoning on biological networks: interpreting transcriptional changes - Chindelevitch et al., section 2. from which the methods and notation is taken.

Usage

CalculateSignificanceUsingQuarticAlgorithm(hypothesisScore, predictionListStats, experimentalDataStats)

Arguments

hypothesisScore

the score for which a p-value is required

predictionListStats

a vector containing the values q+, q- and q0 (the number of positive/negative/non-significant or contradictory) predictions)

experimentalDataStats

a vector containing the values n+, n- and n0 (the number of positive/negative/non-significant (or contradictory) transcripts in the results) (or contradictory) transcripts in the results)

Value

the corresponding p-value

References

L Chindelevitch et al. Causal reasoning on biological networks: Interpreting transcriptional changes. Bioinformatics, 28(8):1114-21, 2012.

Examples

CalculateSignificance(5, c(7,4,19), c(6,6,18))
CalculateSignificance(5, c(7,4,19), c(6,6,18), useCubicAlgorithm=TRUE)
CalculateSignificanceUsingQuarticAlgorithm(5, c(7,4,19), c(6,6,18))
CalculateSignificance(5, c(7,4,19), c(6,6,18), useCubicAlgorithm=FALSE)
CalculateSignificance(5, c(7,4,19), c(6,6,18), 1e-5)
CalculateSignificance(5, c(7,4,19), c(6,6,18), epsilon=1e-5, useCubicAlgorithm=TRUE)
CalculateSignificanceUsingCubicAlgorithm(5, c(7,4,19), c(6,6,18), 1e-5)