enrichment.test: Enrichment test

In elldc/CellTrails: Reconstruction, visualization and analysis of branching trajectories

Description

Statistical enrichment analysis using either a Hypergeometric or Fisher's test

Usage

enrichment.test(
  sample_true,
  sample_size,
  pop_true,
  pop_size,
  method = c("fisher", "hyper")
)

Arguments

sample_true	Number of hits in sample
sample_size	Size of sample
pop_true	Number of hits in population
pop_size	Size of population
method	Statistical method that should be used

Details

Hypergeometric or one-tailed Fisher exact test is useful for enrichment analyses. For example, one needs to estimate which features are enriched among a set of instances sampled from a population.

Value

A list containing the following components:

p.value	P-value of the test
odds.ratio	Odds ratio
conf.int	Confidence interval for the odds ratio (only shown with method="fisher")
method	Used statistical test

Author(s)

Daniel C. Ellwanger

See Also

Hypergeometric and fisher.test

Examples

# Population has 13 of total 52 instances positive for a given feature
# Sample has 1 of total 5 instances positive for a given feature
# Test for significance of enrichment in sample
enrichment.test(sample_true=1, sample_size=5,
                pop_true=13, pop_size=52, method="fisher")

elldc/CellTrails documentation built on May 16, 2020, 4:40 a.m.