calculateMotifEnrichment {transite} | R Documentation

## Binding Site Enrichment Value Calculation

### Description

This function is used to calculate binding site enrichment / depletion scores between predefined foreground and background sequence sets. Significance levels of enrichment values are obtained by Monte Carlo tests.

### Usage

    calculateMotifEnrichment(foreground.scores.df, background.scores.df,
      background.total.sites, background.absolute.hits,
      n.transcripts.foreground, max.fg.permutations = 1e+06,
      min.fg.permutations = 1000, e = 5, p.adjust.method = "BH")

### Arguments

`foreground.scores.df` | result of `scoreTranscripts` on foreground sequence set (foreground sequence sets must be a subset of the background sequence set)
`background.scores.df` | result of `scoreTranscripts` on background sequence set
`background.total.sites` | number of potential binding sites per sequence (returned by `scoreTranscripts`)
`background.absolute.hits` | number of putative binding sites per sequence (returned by `scoreTranscripts`)
`n.transcripts.foreground` | number of sequences in the foreground set
`max.fg.permutations` | maximum number of foreground permutations performed in Monte Carlo test for enrichment score
`min.fg.permutations` | minimum number of foreground permutations performed in Monte Carlo test for enrichment score
`e` | integer-valued 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
`p.adjust.method` | adjustment of p-values from Monte Carlo tests to avoid alpha error accumulation, see `p.adjust`

### Value

A data frame with the following columns:

`motif.id` | the motif identifier that is used in the original motif library
`motif.rbps` | the gene symbol of the RNA-binding protein(s)
`enrichment` | binding site enrichment between foreground and background sequences
`p.value` | unadjusted p-value from Monte Carlo test
`p.value.n` | number of Monte Carlo test permutations
`adj.p.value` | adjusted p-value from Monte Carlo test (usually FDR)

### See Also

Other matrix functions: `runMatrixSPMA`, `runMatrixTSMA`, `scoreTranscriptsSingleMotif`, `scoreTranscripts`

### Examples

    foreground.seqs <- c("CAGUCAAGACUCC", "AAUUGGUGUCUGGAUACUUCCCUGUACAU",
      "AGAU", "CCAGUAA")
    background.seqs <- c(foreground.seqs, "CAACAGCCUUAAUU", "CUUUGGGGAAU",
                         "UCAUUUUAUUAAA", "AUCAAAUUA", "GACACUUAAAGAUCCU",
                         "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA",
                         "AUAGAC", "AGUUC")
    foreground.scores <- scoreTranscripts(foreground.seqs, cache = FALSE)
    background.scores <- scoreTranscripts(background.seqs, cache = FALSE)
    enrichments.df <- calculateMotifEnrichment(foreground.scores$df,
      background.scores$df,
      background.scores$total.sites, background.scores$absolute.hits,
      length(foreground.seqs),
      max.fg.permutations = 1000
    )

[Package transite version 1.0.2 Index]