has_specific_function: find all genomes that complete all of the desired functions

In tbradley1013/KEGGerator: Identify genomic functionality with KEGG

Description

find all genomes that complete all of the desired functions

Usage

has_specific_function(data, function_data, desired_functions)

Arguments

data	a tibble containing all of the orthologies for each genome in a specific pathway. This should be the output of the get_genome_orthologies function
function_data	a tibble containing a function id for each of the orthologies in a desired pathway. An example of this can be seen in the nitrogen_metabolism_orth_fun dataset
desired_functions	a list of vector containing all of the function ids (corresponding to those in the func_id column of the function_data tibble) that a genome should carry out #' @details This function takes two tibbles and a vector. The first (data) is a tibble that is output from get_genome_orthologies. This contains all of the orthologies associated with both the genome and the desired pathway. The second tibble (function_data) contains the function id and function meaning for each orthology in a given pathway. This data should be stored in columns named func_id and func_meaning, respectively. There should also be a column containing the modules that these functions are associated with by the name of modules_name. The third argument (desired_functions) takes a vector or a list of function ids (corresponding to thos in the func_id column in the function_data tibble).

tbradley1013/KEGGerator documentation built on Feb. 23, 2020, 6:44 a.m.