db: Fetch data from remote databases.

In rnabioco/valr: Genome Interval Arithmetic

Fetch data from remote databases.

Description

Currently db_ucsc and db_ensembl are available for connections.

Usage

db_ucsc(
  dbname,
  host = "genome-mysql.cse.ucsc.edu",
  user = "genomep",
  password = "password",
  port = 3306,
  ...
)

db_ensembl(
  dbname,
  host = "ensembldb.ensembl.org",
  user = "anonymous",
  password = "",
  port = 3306,
  ...
)

Arguments

dbname	name of database
host	hostname
user	username
password	password
port	MySQL connection port
...	params for connection

See Also

https://genome.ucsc.edu/goldenpath/help/mysql.html

https://www.ensembl.org/info/data/mysql.html

Examples

## Not run: 
if (require(RMariaDB)) {
  library(dplyr)
  ucsc <- db_ucsc("hg38")

  # fetch the `refGene` tbl
  tbl(ucsc, "refGene")

  # the `chromInfo` tbls have size information
  tbl(ucsc, "chromInfo")
}

## End(Not run)
## Not run: 
if (require(RMariaDB)) {
  library(dplyr)
  # squirrel genome
  ensembl <- db_ensembl("spermophilus_tridecemlineatus_core_67_2")

  tbl(ensembl, "gene")
}

## End(Not run)

rnabioco/valr documentation built on April 9, 2024, 3:26 p.m.