calculate_kmer_enrichment {transite} | R Documentation |
Calls compute_kmer_enrichment
to compute k-mer
enrichment values
for multiple foregrounds. Calculates enrichment for foreground sets in
parallel.
calculate_kmer_enrichment( foreground_sets, background_set, k, permutation = FALSE, chisq_p_value_threshold = 0.05, p_adjust_method = "BH", n_cores = 4 )
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 |
character vector of DNA or RNA sequences that constitute the background set |
k |
length of k-mer, either |
permutation |
if |
chisq_p_value_threshold |
threshold below which Fisher's exact test is used instead of Pearson's chi-squared test |
p_adjust_method |
see |
n_cores |
number of computing cores to use |
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 |
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()
# 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)