Test for Enrichment

Calculated whether 2x2 table is enriched for a particular group using Hypergeometric Distribution and the Fisher's Exact test for count data.

Usage

enrich_test(x, ...)

# S3 method for class 'list'
enrich_test(x, ...)

# S3 method for class 'data.frame'
enrich_test(x, ...)

# S3 method for class 'matrix'
enrich_test(x, ...)

Arguments

x: A 2x2 confusion matrix (aka contingency table) containing the binary decisions for each contingency (or a similarly structured data frame). Can also be a (named) list containing each of the 4 contingencies. See examples.
...: Arguments passed to stats::fisher.test(). In particular, alternative which determines whether to check for both enrichment and depletion ("two.sided") or specifically one or the other: enrichment = "greater"; depletion = "less".

Value

An "enrichment" class object, a list of the significance tests calculated from a Hypergeometric Distribution stats::dhyper() as well as those calculated via Fisher's Exact stats::fisher.test() test for count data testing the H_o that the odds ratio is equal to 1. The p-values for various flavors of Hypergeometric test are:

1-sided: add here.
2-sided: double of 1-sided.
1-sided mid: add description
2-sided mid: double of 1-sided mid.
2-sided min lik: this differs previous, but is most similar to Fisher's Exact
2-sided min lik mid: this is typically preferred

Details

Can also pass a named list containing:

`n11`	:	The corresponding `[1,1]` position of the `2x2` matrix.
`n1_`	:	The sum of the top row of the table.
`n_1`	:	The sum of the first column of the table.
`n`	:	The sum of the table.

Author

Stu Field

Examples

c_mat <- matrix(c(4, 2, 3, 11), ncol = 2L)
enrich_test(c_mat)
#> ══ Enrichment Tests ══════════════════════════════════════════════════════
#> ── Counts Table ──────────────────────────────────────────────────────────
#>      v2
#> v1    no yes
#>   no   4   3
#>   yes  2  11
#> 
#> ── Hypergeometric ────────────────────────────────────────────────────────
#> ℹ Test-type            p-value
#> 
#> • 1-sided              0.07765738
#> • 2-sided              0.15531476
#> • 1-sided mid          0.04244066
#> • 2-sided mid          0.08488132
#> • 2-sided min lik      0.12192982
#> • 2-sided min lik mid★ 0.08671311
#> 
#> ── Fisher's Exact ────────────────────────────────────────────────────────
#> ℹ Alternative          two.sided
#> 
#> • Odds Ratio           6.48649744
#> • Odds Ratio p-value   0.12192982
#> • OR CI95              [0.601, 107.532]
#> ══════════════════════════════════════════════════════════════════════════

# or pass a named list
en_list <- list(n11 = 4, n1_ = 7, n_1 = 6, n = 20)
enrich_test(en_list)
#> ══ Enrichment Tests ══════════════════════════════════════════════════════
#> ── Counts Table ──────────────────────────────────────────────────────────
#>      v2
#> v1    no yes
#>   no   4   3
#>   yes  2  11
#> 
#> ── Hypergeometric ────────────────────────────────────────────────────────
#> ℹ Test-type            p-value
#> 
#> • 1-sided              0.07765738
#> • 2-sided              0.15531476
#> • 1-sided mid          0.04244066
#> • 2-sided mid          0.08488132
#> • 2-sided min lik      0.12192982
#> • 2-sided min lik mid★ 0.08671311
#> 
#> ── Fisher's Exact ────────────────────────────────────────────────────────
#> ℹ Alternative          two.sided
#> 
#> • Odds Ratio           6.48649744
#> • Odds Ratio p-value   0.12192982
#> • OR CI95              [0.601, 107.532]
#> ══════════════════════════════════════════════════════════════════════════