generate_permuted_enrichments {transite} | R Documentation

## Generate Random Permutations of the Enrichment Data

### Description

Calculates k-mer enrichment values for randomly sampled (without replacement) foreground sets.

### Usage

    generate_permuted_enrichments(
      n_transcripts_foreground,
      background_set,
      k,
      n_permutations = 1000,
      n_cores = 4
    )

### Arguments

`n_transcripts_foreground` | number of transcripts in the original foreground 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
`n_permutations` | number of permutations to perform
`n_cores` | number of computing cores to use

### Value

The result of `calculate_kmer_enrichment` for the random foreground sets.

### See Also

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

[Package transite version 1.8.0 Index]