get_sim_p {ontologySimilarity}

Get similarity p-value

Description

p-value of group similarity, calculated by estimating the proportion by random sampling of groups the same size as group which have at least as great group similarity than does group.

Usage

get_sim_p(pop_sim, ...)

## S3 method for class 'integer'
get_sim_p(pop_sim, ...)

## S3 method for class 'numeric'
get_sim_p(pop_sim, group, ...)

## S3 method for class 'matrix'
get_sim_p(pop_sim, group, ...)

## S3 method for class 'sim_index'
get_sim_p(pop_sim, group, ...)

## Default S3 method:
get_sim_p(
  pop_sim,
  group,
  type,
  min_its = 1000,
  max_its = 1e+05,
  signif = 0.05,
  log_dismiss = log(1e-06),
  group_sim = "average",
  ...
)

Arguments

pop_sim

An object representing the similarities of an indexed population of objects.

...

Arguments for get_sim_p.

group

Character or integer vector specifying names/indices of subgroup for which to calculate a group similarity p-value.

type

Either "matrix", "sim_index" or "numeric" - the type of the pop_sim object.

min_its

Minimum number of simulated group similarities to calculate

max_its

Maximum number of simulated group similarities to calculate

signif

Threshold p-value of statistical significance

log_dismiss

Threshold of log probability, below which to trigger return of current estimated p-value

group_sim

String Either "average" or "min", determining how to calculate the similarity of a group of term sets over all pairwise combinations of group members

Value

p-value.

See Also

get_sim sample_group_sim