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 1.0.2 Index]