calculatePvalue: p-value that two PWM-positions are from the same distribution
In mgledi/DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description Usage Arguments Value Author(s) Examples

Calculates the p-value for the null-hypothesis that two given probability vectors p1, p2 calculated from n1/n2 observations arise from the same distribution

1 2	calculatePvalue(p1, p2, n1, n2, stackHeight = shannonDivergence, numberOfPermutations = 100, plotGammaDistributionFit = FALSE)

`p1`	first probability vector with one probability for each symbol of the alphabet
`p2`	second probability vector with one probability for each symbol of the alphabet
`n1`	number of observations for the calculation of p1
`n2`	number of observations for the calculation of p2
`stackHeight`	function for the calculation of a divergence measure for two probability vectors
`numberOfPermutations`	the number of permutations to perform for the calculation of stackHeights
`plotGammaDistributionFit`	if TRUE the fit of a gamma distribution to the sampled stackHeights is plotted

a numeric p-value

Hendrik Treutler

p1 <- c(0.2, 0.3, 0.1, 0.4)
p2 <- c(0.2, 0.1, 0.3, 0.4)
n1 <- 100
n2 <- 200
numberOfPermutations = 100
plotGammaDistributionFit = TRUE

pValue <- calculatePvalue(p1 = p1, p2 = p2, n1 = n1, n2 = n2, stackHeight = shannonDivergence, numberOfPermutations = numberOfPermutations, plotGammaDistributionFit = plotGammaDistributionFit)