generatePermutedEnrichments {transite} | R Documentation

## Generate Random Permutations of the Enrichment Data

### Description

Calculates k-mer enrichment values for randomly sampled (without replacement) foreground sets.

### Usage

    generatePermutedEnrichments(n.transcripts.foreground, background.set, k,
      n.permutations = 1000, n.cores = 4)

### Arguments

`n.transcripts.foreground` | number of transcripts in the original foreground set
`background.set` | character vector of DNA or RNA sequences that constitute the background set
`k` | length of k-mer, either `6` for hexamers or `7` for heptamers
`n.permutations` | number of permutations to perform
`n.cores` | number of computing cores to use

### Value

The result of `calculateKmerEnrichment` for the random foreground sets.

### See Also

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

[Package transite version 1.2.1 Index]