knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
regulonDB package takes an RSQLite object imported previously from an SQLite database file to R.
This step sholud be executed by the user before use the functions of regulonDB package. An example to load to R the SQLite object is:
path_sqlite3 <- file.choose() regulon <- DBI::dbConnect(RSQLite::SQLite(), path_sqlite3)
Prints all marts contained in the SQL object
listDatasets(regulon)
Prints a list of the columns of the mart
listAttributes(regulon, "TF")
Allows users to filter and retrieve data from a particular mart from SQLite database.
getAttr( database = regulon, mart = "GENE", filters = c("operon_id", "operon_name"), value = c("ECK125235983","cmoM-mukFEB" ), cond = "and")
Shows all the genes regulated by a Transcription Factor indicated by the user
GetRegulatedGenesByTF(regulon, "Ara")
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