enrichment_fisher: evaluates KO enrichment using the fisher test
In josschavezf/erba: erba: Expression Regulators from Bacteria and Archaea

Description Usage Arguments Value Examples

Takes a data.frame and a vector with column names contained in the data.frame. Performs the fisher test to evaluate enrichement per KO per phylogenetic group from selected phylogeny.

enrichment_fisher(
  x,
  column_names,
  replace_by = NULL,
  phylogeny = selected_phylogeny
)

`x`	data frame where the test will be applied.
`column_names`	Vector with column names to include in the test
`replace_by`	Replace the Inf values in the odd.ratio matrix by a value.
`phylogeny`	Vector of phylogenetic groups or rownames to include in the test

a list with two matrixes: p.value and odd.ratio.

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my_data <- erba::sigma_filtered
fisher_evaluation <- enrichment_fisher(sigma_filtered, kos_sigma)
fisher_evaluation <- enrichment_fisher(sigma_filtered, kos_sigma, replace_by  = 100)