calculate_transcript_mc: Motif Enrichment calculation

In kkrismer/transite: RNA-binding protein motif analysis

Motif Enrichment calculation

Description

C++ implementation of Motif Enrichment calculation

Usage

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

Arguments

absoluteHits	number of putative binding sites per sequence (returned by score_transcripts)
totalSites	number of potential binding sites per sequence (returned by score_transcripts)
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 <- get_motif_by_id("M178_0.6")
fg <- score_transcripts(foreground_seqs, cache = FALSE,
  motifs = motif_db)
bg <- score_transcripts(background_seqs, cache = FALSE,
  motifs = motif_db)

mc_result <- calculate_transcript_mc(unlist(bg$absolute_hits),
 unlist(bg$total_sites),
 fg$df$absolute_hits / fg$df$total_sites,
 length(foreground_seqs), 1000, 500, 5)

kkrismer/transite documentation built on July 13, 2024, 8:01 a.m.