CalculateSignificanceUsingCubicAlgorithm1b: Calculate Significance Using Cubic Algorithm

Description Usage Arguments Value Examples

Description

Calculate the p-value of a score given the hypothesis score and the distribution table (calculated using the cubic algorithm 1b in Assessing statistical significance in causal graphs - Chindelevitch et al)

Usage

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CalculateSignificanceUsingCubicAlgorithm1b(hypothesisScore, predictionListStats,
  experimentalDataStats, epsilon)

Arguments

hypothesisScore

The score whose p-value we want to find.

predictionListStats

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

experimentalDataStats

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

epsilon

The threshold that is used when calculating the p-value using the cubic algorithm. (Defaults to 1e-5, only used for the cubic algorithm, ignored if useCubicAlgorithm is FALSE.)

Value

p value

Examples

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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)
CalculateSignificanceUsingCubicAlgorithm1b(5, c(7,4,19), c(6,6,18), 1e-5)


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