generate_permuted_enrichments: Generate Random Permutations of the Enrichment Data

View source: R/k-mer-based.R

generate_permuted_enrichmentsR 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(), create_kmer_origin_list(), draw_volcano_plot(), estimate_significance(), estimate_significance_core(), generate_kmers(), run_kmer_spma(), run_kmer_tsma()


kkrismer/transite documentation built on July 13, 2024, 8:01 a.m.