group_term_enrichment | R Documentation |
Create a table of terms ranked by their significance of occurrence in a set of term sets amongst an enclosing set, with p-values computed by permutation. Terms are subselected so that only the minimal set of non-redundant terms at each level of frequency within the group are retained.
group_term_enrichment(
ontology,
term_sets,
group,
permutations = 1000L,
min_terms = 2L,
mc.cores = NULL
)
ontology |
|
term_sets |
List of character vectors of ontological term IDs. |
group |
Integer/logical/character vector specifying indices/positions/names of subgroup for which to calculate a group similarity p-value. |
permutations |
Number of permutations to test against, or if |
min_terms |
Minimum number of times a term should occur within the given group to be eligible for inclusion in the results. |
mc.cores |
If not null and greater than on, the number of cores use calculating permutations (passed to |
data.frame
containing columns: term
(with the term ID); name
(term readable name); in_term
(number of sets in the given group of containing the term); in_no_term
(number of sets in the given group not containing the term); out_term
and out_no_term
(equivalently for the sets not in the given group); p
(the p-values calculated by permutation for seeing a term with such a strong association, measured using Fisher's exact test, in a group of term sets the size of the given group among term_sets
). Rows ordered by significance (i.e. the p
columns).
sample_group_sim
create_sim_index
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