get_dataset {regutools} | R Documentation |
This function retrieves data from RegulonDB. Attributes from datasets can be selected and filtered.
get_dataset( regulondb, dataset = NULL, attributes = NULL, filters = NULL, and = TRUE, interval = NULL, partialmatch = NULL, output_format = "regulondb_result" )
regulondb |
A |
dataset |
Dataset of interest. Use the function list_datasets for an overview of valid datasets. |
attributes |
Vector of attributes to be retrieved. |
filters |
List of filters to be used. The names should correspond to the attribute and the values correspond to the condition for selection. |
and |
Logical argument. If FALSE, filters will be considered under the "OR" operator |
interval |
the filters whose values will be considered as interval |
partialmatch |
name of the condition(s) with a string pattern for full or partial match in the query |
output_format |
A string specifying the output format. Possible options are "regulondb_result", "GRanges", "DNAStringSet" or "BStringSet". |
By default, a regulon_results object. If specified in the parameter output_format, it can also return either a GRanges object or a Biostrings object.
Carmina Barberena Jonas, Jesús Emiliano Sotelo Fonseca, José Alquicira Hernández, Joselyn Chávez
## 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" ) ## Obtain all the information from the "GENE" dataset get_dataset(e_coli_regulondb, dataset = "GENE") ## Get the attributes posright and name from the "GENE" dataset get_dataset(e_coli_regulondb, dataset = "GENE", attributes = c("posright", "name") ) ## From "GENE" dataset, get the gene name, strand, posright, product name ## and id of all genes regulated with name like "ara", strand as "forward" ## with a position right between 2000 and 40000 get_dataset( e_coli_regulondb, dataset = "GENE", attributes = c("name", "strand", "posright", "product_name", "id"), filters = list( name = c("ara"), strand = c("forward"), posright = c("2000", "40000") ), and = TRUE, partialmatch = "name", interval = "posright" )