estimate_significance: Permutation Test Based Significance of Observed Mean

Description Usage Arguments Value See Also

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

Description

estimate_significance returns an estimate of the significance of the observed mean, given a set of random permutations of the data.

Usage

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estimate_significance(
  actual_mean,
  motif_kmers,
  random_permutations,
  alternative = c("two_sided", "less", "greater"),
  conf_level = 0.95,
  produce_plot = TRUE
)

Arguments

actual_mean

observed mean

motif_kmers

set of k-mers that were used to compute the actual_mean

random_permutations

a set of random permutations of the original data, used to generate an empirical null distribution.

alternative

side of the test, one of the following: "two_sided", "less", "greater"

conf_level

confidence level for the returned confidence interval

produce_plot

if distribution plot should be part of the returned list

Value

A list with the following components:

p_value_estimate the estimated p-value of the observed mean
conf_int the confidence interval around that estimate
plot plot of the empirical distribution of geometric means of the enrichment values

See Also

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


transite documentation built on Nov. 8, 2020, 5:27 p.m.