permTestGeometricMean {transite}R Documentation

Permutation Test Based Significance of Observed Mean

Description

permTestGeometricMean returns an estimate of the significance of the observed mean, given a set of random permutations of the data.

Usage

permTestGeometricMean(actual.mean, motif.kmers, random.permutations,
  alternative = c("two.sided", "less", "greater"), conf.level = 0.95,
  produce.plot = TRUE)

Arguments

actual.mean

observed mean

motif.kmers

set of k-mers that were used to compute the actual.mean

random.permutations

a set of random permutations of the original data, used to generate an empirical null distribution.

alternative

side of the test, one of the following: "two.sided", "less", "greater"

conf.level

confidence level for the returned confidence interval.

produce.plot

if distribution plot should be part of the returned list

Value

A list with the following components:

p.value.estimate the estimated p-value of the observed mean
conf.int the confidence interval around that estimate
plot plot of the empirical distribution of geometric means of the enrichment values

See Also

Other k-mer functions: calculateKmerEnrichment, checkKmers, computeKmerEnrichment, drawVolcanoPlot, empiricalEnrichmentMeanCDF, generateKmers, generatePermutedEnrichments, homopolymerCorrection, runKmerSPMA, runKmerTSMA


[Package transite version 1.2.0 Index]