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 1.2.0 Index]