calculate_motif_enrichment {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

    calculate_motif_enrichment(
      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 `score_transcripts` on foreground sequence set (foreground sequence sets must be a subset of the background sequence set)
`background_scores_df` | result of `score_transcripts` on background sequence set
`background_total_sites` | number of potential binding sites per sequence (returned by `score_transcripts`)
`background_absolute_hits` | number of putative binding sites per sequence (returned by `score_transcripts`)
`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: `run_matrix_spma()`, `run_matrix_tsma()`, `score_transcripts_single_motif()`, `score_transcripts()`

### 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 <- score_transcripts(foreground_seqs, cache = FALSE)
    background_scores <- score_transcripts(background_seqs, cache = FALSE)
    enrichments_df <- calculate_motif_enrichment(foreground_scores$df,
      background_scores$df,
      background_scores$total_sites, background_scores$absolute_hits,
      length(foreground_seqs),
      max_fg_permutations = 1000
    )

[Package transite version 1.10.0 Index]