calculatePvalue {DiffLogo} | R Documentation

## p-value that two PWM-positions are from the same distribution

### Description

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

### Usage

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

### Arguments

`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

### Value

a numeric p-value

### Author(s)

Hendrik Treutler

### Examples

    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)

[Package DiffLogo version 2.6.0 Index]