List the modules corresponding to a given object of interest

Usage

identify_module(
  object_of_interest,
  annotation_table,
  col_module_id,
  annotation_level = "species"
)

Arguments

object_of_interest: String. The name of the bacteria or species of interest or a key word in the functional module definition
annotation_table: Dataframe. The dataframe gathering the taxonomic or functional module correspondence information
col_module_id: String. The name of the column with the module names in the annotation table
annotation_level: String. The name of the column with the level to be studied. Examples: species, genus, level_1. Default value is set to the species level

Value

List of string. The module names of the corresponding object of interest

Examples

df_taxo <- data.frame(
  msp_name = c("msp_1", "msp_2", "msp_3", "msp_4"),
  genus = c("One", "One", "One", "Two"),
  species = c("One bacteria", "One bacterium L", "One bacterium G", "Two bact")
)
identify_module(object_of_interest = "bacterium", annotation_table = df_taxo, col_module_id = "msp_name", annotation_level = "species")
#> [1] "msp_2" "msp_3"
identify_module(object_of_interest = "One", annotation_table = df_taxo, col_module_id = "msp_name", annotation_level = "species")
#> [1] "msp_1" "msp_2" "msp_3"