List all attributes and their description of a dataset from
RegulonDB. The result of this function may
be used as parameter 'values' in list_attributes() function.
list_attributes(regulondb, dataset)A regulondb() object.
Dataset of interest. The name should correspond to a table of the database.
A character vector with the field names.
## Connect to the RegulonDB database if necessary
if (!exists("regulondb_conn")) regulondb_conn <- connect_database()
## Build the regulon db object
e_coli_regulondb <-
regulondb(
database_conn = regulondb_conn,
organism = "E.coli",
database_version = "1",
genome_version = "1"
)
## List the transcription factor attributes
list_attributes(e_coli_regulondb, "TF")
#> [1] "id" "name"
#> [3] "synonyms" "encode_tf_gene_id"
#> [5] "encode_tf_operon_id" "encode_tf_tu_id"
#> [7] "site_length" "symmetry"
#> [9] "transcription_factor_family" "connectivity_class"
#> [11] "sensing_class" "global_function_all_tfbs"
#> [13] "global_function_strong" "note"
#> [15] "total_regulated_gene" "total_effect_repressor_gene"
#> [17] "total_effect_activator_gene" "total_effect_dual_gene"
#> [19] "total_effect_unknown_gene" "total_tfbs"
#> [21] "total_ri" "total_regulated_tf"
#> [23] "total_regulated_promoter" "total_regulated_tu"
#> [25] "total_regulated_operon" "total_coregulated_sigma"
#> [27] "total_active_conformation" "total_coregulator"
#> [29] "regulated_gene_info" "regulated_tf_id"
#> [31] "regulated_tf_name" "regulated_tu_id"
#> [33] "regulated_tu_name" "regulated_operon_id"
#> [35] "regulated_operon_name" "regulated_pm_id"
#> [37] "regulated_pm_name" "coregulated_sigma"
#> [39] "active_conformation_id" "active_conformation_name"
#> [41] "coregulator_id" "coregulator_name"
#> [43] "tfbs_unique" "regulation_info"
#> [45] "evidence_reference"
## List the operon attributes
list_attributes(e_coli_regulondb, "OPERON")
#> [1] "id" "name" "firstgeneposleft"
#> [4] "lastgeneposright" "regulationposleft" "regulationposright"
#> [7] "strand" "total_tu" "total_gene"
#> [10] "total_sigma" "total_promoter" "total_tfbs"
#> [13] "total_ri" "total_tf" "total_terminator"
#> [16] "tu_id" "tu_name" "gene_info"
#> [19] "sigma_name" "promoter_name" "tf_name"
#> [22] "ri_id" "ri_info" "tm_ids"