has_complete_function: returns genomes that have all the functions in specified...
In tbradley1013/KEGGerator: Identify genomic functionality with KEGG

returns genomes that have all the functions in specified module

1	has_complete_function(data, function_data, complete_functions)

`data`	a tibble that is output from `get_genome_orthologies()`
`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
`complete_functions`	a tibble containing all of the functions required for each full process in a given pathway. An example can be seen in the `nitrogen_metabolism_fun_groups` dataset

This function takes three tibbles. 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 thibble (complete_functions) should be a tibble with two columns. The first column should be named modules_name and there should be a row for every module in a specific pathway. The second column should be named funcs_in_module and should be a list column where each row contains a list with all of the function ids (corresponding to the func_id column in the function_data dataset)

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