Create a Differential Abundance Result Object

Wrap a tidy differential abundance table in a standard result class used by plotting helpers.

Usage

create_differential_abundance_result(
  result,
  method = "external",
  taxonomic_rank = "",
  group = ""
)

Arguments

result

A data.frame containing at least variable_id and estimate.

method

Differential abundance method label.

taxonomic_rank

Taxonomic level represented in the result.

group

Optional comparison label.

Value

A differential_abundance_result object.

Examples

data("global_patterns", package = "microbiomedataset")

x0 <- prune_taxa(global_patterns, variable_id = global_patterns@variable_info$variable_id[1:200])
genus_object <- summarise_taxa(x0, taxonomic_rank = "Genus")
result_table <- data.frame(
  variable_id = genus_object@variable_info$variable_id[1:10],
  estimate = seq(-2, 2, length.out = 10),
  p_value = seq(0.01, 0.1, length.out = 10),
  q_value = seq(0.02, 0.2, length.out = 10)
)
da_result <- create_differential_abundance_result(
  result = cbind(result_table, genus_object@variable_info[1:10, ]),
  method = "external",
  taxonomic_rank = "Genus"
)
da_result
#> differential_abundance_result
#> Method: external
#> Taxonomic rank: Genus
#> Rows: 10