find_working_mart: Find a functional biomart instance.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Find a functional biomart instance.

Description

In my experience, the various biomart mirrors are not varyingly likely to be functional at any given time. In addition, I often find it useful to use an archive instance rather than the most recent ensembl instance. This function therefore iterates over the various mirrors; or if archive = TRUE it will try a series of archive servers from 1, 2, and 3 years ago.

Usage

find_working_mart(
  default_hosts = c("useast.ensembl.org", "uswest.ensembl.org", "www.ensembl.org",
    "asia.ensembl.org"),
  trymart = "ENSEMBL_MART_ENSEMBL",
  archive = FALSE,
  year = NULL,
  month = NULL
)

Arguments

default_hosts	List of biomart mirrors to try.
trymart	Specific mart to query.
archive	Try an archive server instead of a mirror? If this is a character, it will assume it is a specific archive hostname.
year	Choose specific year(s) for the archive servers?
month	Choose specific month(s) for the archive servers?

Value

Either a mart instance or NULL if no love was forthcoming.

See Also

[biomaRt::useMart()] [biomaRt::listMarts()]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.