generate_permuted_enrichments: Generate Random Permutations of the Enrichment Data

In kkrismer/transite: RNA-binding protein motif analysis

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(), estimate_significance_core(), generate_kmers(), run_kmer_spma(), run_kmer_tsma()

kkrismer/transite documentation built on Feb. 9, 2024, 3:23 a.m.