CausalR (version 1.4.3)

CalculateSignificanceUsingCubicAlgorithm: calculate significance using the cubic algorithm

Description

Calculates the p-value of a score given the hypothesis score and the distribution table (calculated using the cubic algorithm)

Usage

CalculateSignificanceUsingCubicAlgorithm(hypothesisScore, predictionListStats, experimentalDataStats, epsilon)

Arguments

hypothesisScore

the score whose p-value we want to find.

predictionListStats

numbers of predicted up-regulated, predicted down-regulated and ambiguous predictions.

experimentalDataStats

numbers of up-regulated, down-regulated and not significantly changed transcripts in the experimental data.

epsilon

an epsilon threshold that is used when calculating the p-value using the cubic algorithm. Defaults to 1e-5.

Value

p-value

References

L Chindelevitch et al. Assessing statistical significance in causal graphs. BMC Bioinformatics, 13(35), 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)