calculateTranscriptMC {transite} | R Documentation |
C++ implementation of Motif Enrichment calculation
calculateTranscriptMC(absoluteHits, totalSites, relHitsForeground, n, maxPermutations, minPermutations, e)
absoluteHits |
number of putative binding sites per sequence
(returned by |
totalSites |
number of potential binding sites per sequence
(returned by |
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 |
list with p-value and number of iterations of Monte Carlo sampling for foreground enrichment
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)