get_gene_regulators {regutools} | R Documentation |
Given a list of genes (name, bnumber or GI), get all transcription factors or genes that regulate them. The effect of regulators over the gene of interest can be positive (+), negative (-) or dual (+/-)
get_gene_regulators(regulondb, genes, format = "multirow", output.type = "TF")
regulondb |
A regulondb class. |
genes |
Vector of genes (name, bnumber or GI). |
format |
Output format: multirow, onerow, table |
output.type |
How regulators will be represented: "TF"/"GENE" |
A regulondb_result 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" ) ## Get Transcription factors that regulate araC in one row get_gene_regulators( e_coli_regulondb, genes = c("araC"), output.type = "TF", format = "onerow" ) ## Get genes that regulate araC in table format get_gene_regulators( e_coli_regulondb, genes = c("araC"), output.type = "GENE", format = "table" )