calculate overall significance p-value

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Description

Calculates the p-value of a score given the hypothesis score and the distribution table, using either the quartic or the (faster) cubic algorithm

Usage

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CalculateSignificance(hypothesisScore, predictionListStats,
  experimentalResultStats, epsilon = 1e-05, useCubicAlgorithm = TRUE,
  use1bAlgorithm = TRUE)

Arguments

hypothesisScore

score for a particular hypothesis

predictionListStats

numbers of predicted up-regulated, predicted down-regulated and ambiguous predictions predicted by the algorithm

experimentalResultStats

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

epsilon

threshold that is used when calculating the p-value using the cubic algorithm

useCubicAlgorithm

use the cubic algorithm, defaults to TRUE

use1bAlgorithm

use the 1b version of the algorithm, defaults to TRUE used to calculate the p-value

Value

the resulting 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)
CalculateSignificanceUsingCubicAlgorithm(5, c(7,4,19), c(6,6,18), 1e-5)

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