calculateTranscriptMC {transite}R Documentation

Motif Enrichment calculation

Description

C++ implementation of Motif Enrichment calculation

Usage

calculateTranscriptMC(absoluteHits, totalSites, relHitsForeground, n,
  maxPermutations, minPermutations, e)

Arguments

absoluteHits

number of putative binding sites per sequence (returned by scoreTranscripts)

totalSites

number of potential binding sites per sequence (returned by scoreTranscripts)

relHitsForeground

relative number of hits in foreground set

n

number of sequences in the foreground set

maxPermutations

maximum number of foreground permutations performed in Monte Carlo test for enrichment score

minPermutations

minimum number of foreground permutations performed in Monte Carlo test for enrichment score

e

stop criterion for enrichment score Monte Carlo test: aborting permutation process after observing e random enrichment values with more extreme values than the actual enrichment value

Value

list with p-value and number of iterations of Monte Carlo sampling for foreground enrichment

Examples

foreground.seqs <- c("CAGUCAAGACUCC", "AAUUGGUUGUGGGGCUUCCCUGUACAU",
                     "AGAU", "CCAGUAA", "UGUGGGG")
background.seqs <- c(foreground.seqs, "CAACAGCCUUAAUU", "CUUUGGGGAAU",
                     "UCAUUUUAUUAAA", "AUCAAAUUA", "GACACUUAAAGAUCCU",
                     "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA",
                     "AUAGAC", "AGUUC")
motif.db <- getMotifById("M178_0.6")
fg <- scoreTranscripts(foreground.seqs, cache = FALSE,
  motifs = motif.db)
bg <- scoreTranscripts(background.seqs, cache = FALSE,
  motifs = motif.db)

mc.result <- calculateTranscriptMC(unlist(bg$absolute.hits),
 unlist(bg$total.sites),
 fg$df$absolute.hits / fg$df$total.sites,
 length(foreground.seqs), 1000, 500, 5)
[Package transite version 1.5.0 Index]