computeKmerEnrichment {transite}R Documentation

k-mer Enrichment between Foreground and Background Sets

Description

Compares foreground sequence set to background sequence set and computes enrichment values for each possible k-mer.

Usage

computeKmerEnrichment(foreground.kmers, background.kmers,
  permutation = FALSE, chisq.p.value.threshold = 0.05,
  p.adjust.method = "BH")

Arguments

foreground.kmers

k-mer counts of the foreground set (generated by generateKmers)

background.kmers

k-mer counts of the background set (generated by generateKmers)

permutation

if TRUE, only the enrichment value is returned (efficiency mode used for permutation testing)

chisq.p.value.threshold

threshold below which Fisher's exact test is used instead of Pearson's chi-squared test

p.adjust.method

see p.adjust

Details

Usually uses Pearson's chi-squared test, but recalculates p-values with Fisher's exact test for Pearson's chi-squared test p-values <= chisq.p.value.threshold. The reason this is done is computational efficiency. Fisher's exact tests are computationally demanding and are only performed in situations, where exact p-values are preferred, e.g., if expected < 5 or significant p-values.

Value

enrichment of k-mers in specified foreground sequences. A data frame with the following columns is returned:

foreground.count foreground counts for each k-mer
background.count background counts for each k-mer
enrichment k-mer enrichment
p.value p-value of k-mer enrichment (either from Fisher's exact test or Pearson's chi-squared test.
adj.p.value multiple testing corrected p-value

See Also

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

Examples

# define simple sequence sets for foreground and background
foreground.set <- c(
  "CAACAGCCUUAAUU", "CAGUCAAGACUCC", "CUUUGGGGAAU",
  "UCAUUUUAUUAAA", "AAUUGGUGUCUGGAUACUUCCCUGUACAU",
  "AUCAAAUUA", "AGAU", "GACACUUAAAGAUCCU",
  "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA",
  "AUAGAC", "AGUUC", "CCAGUAA"
)
background.set <- c(
  "CAACAGCCUUAAUU", "CAGUCAAGACUCC", "CUUUGGGGAAU",
  "UCAUUUUAUUAAA", "AAUUGGUGUCUGGAUACUUCCCUGUACAU",
  "AUCAAAUUA", "AGAU", "GACACUUAAAGAUCCU",
  "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA",
  "AUAGAC", "AGUUC", "CCAGUAA",
  "UUAUUUA", "AUCCUUUACA", "UUUUUUU", "UUUCAUCAUU",
  "CCACACAC", "CUCAUUGGAG", "ACUUUGGGACA", "CAGGUCAGCA"
)
foreground.kmers <- generateKmers(foreground.set, 6)
background.kmers <- generateKmers(background.set, 6)


kmer.enrichment.values <- computeKmerEnrichment(foreground.kmers,
  background.kmers)

[Package transite version 1.2.0 Index]