calculate_kmer_enrichment {transite} | R Documentation

## k-mer Enrichment between Foreground and Background Sets

### Description

Calls `compute_kmer_enrichment` to compute k-mer enrichment values for multiple foregrounds. Calculates enrichment for foreground sets in parallel.

### Usage

    calculate_kmer_enrichment(
      foreground_sets,
      background_set,
      k,
      permutation = FALSE,
      chisq_p_value_threshold = 0.05,
      p_adjust_method = "BH",
      n_cores = 4
    )

### Arguments

`foreground_sets` | list of foreground sets; a foreground set is a character vector of DNA or RNA sequences (not both) and a strict subset of the `background_set`
`background_set` | character vector of DNA or RNA sequences that constitute the background set
`k` | length of k-mer, either `6` for hexamers or `7` for heptamers
`permutation` | if `TRUE`, only the enrichment value is returned (efficiency mode used for permutation testing)
`chisq_p_value_threshold` | threshold below which Fisher's exact test is used instead of Pearson's chi-squared test
`p_adjust_method` | see `p.adjust`
`n_cores` | number of computing cores to use

### Value

A list with two entries:

`dfs` | a list of data frames with results from `compute_kmer_enrichment` for each of the foreground sets
`kmers` | a character vector of all k-mers

### See Also

Other k-mer functions: `check_kmers()`, `compute_kmer_enrichment()`, `count_homopolymer_corrected_kmers()`, `draw_volcano_plot()`, `estimate_significance_core()`, `estimate_significance()`, `generate_kmers()`, `generate_permuted_enrichments()`, `run_kmer_spma()`, `run_kmer_tsma()`

### Examples

    # define simple sequence sets for foreground and background
    foreground_set1 <- c(
      "CAACAGCCUUAAUU", "CAGUCAAGACUCC", "CUUUGGGGAAU",
      "UCAUUUUAUUAAA", "AAUUGGUGUCUGGAUACUUCCCUGUACAU",
      "AUCAAAUUA", "AGAU", "GACACUUAAAGAUCCU",
      "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA",
      "AUAGAC", "AGUUC", "CCAGUAA"
    )
    foreground_set2 <- c("UUAUUUA", "AUCCUUUACA", "UUUUUUU", "UUUCAUCAUU")
    foreground_sets <- list(foreground_set1, foreground_set2)
    background_set <- c(foreground_set1, foreground_set2,
                        "CCACACAC", "CUCAUUGGAG", "ACUUUGGGACA", "CAGGUCAGCA")

    # single-threaded
    kmer_enrichment_values_st <- calculate_kmer_enrichment(foreground_sets,
      background_set, 6, n_cores = 1)
    ## Not run:
    # multi-threaded
    kmer_enrichment_values_mt <- calculate_kmer_enrichment(foreground_sets,
      background_set, 6)
    ## End(Not run)

[Package transite version 1.10.0 Index]