In josschavezf/regulonDB: Management of SQLite Databases and Query of Fields tools

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

regulonDB package takes an RSQLite object imported previously from an SQLite database file to R.

Shows datasets available in the database and the fields of the data.
Filter specific fields and search for rows that match with specific characteristics.

Libraries needed

RSQLite
DBI
dplyr
dbplyr

Import an SQLite dataset

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)

listDatasets

Prints all marts contained in the SQL object

  listDatasets(regulon)

listAttributes

Prints a list of the columns of the mart

  listAttributes(regulon, "TF")

getAttr

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")