load_biomart_orthologs: Use biomart to get orthologs between supported species.

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

Use biomart to get orthologs between supported species.

Description

Biomart's function getLDS is incredibly powerful, but it makes me think very polite people are going to start knocking on my door, and it fails weirdly pretty much always. This function attempts to alleviate some of that frustration.

Usage

load_biomart_orthologs(
  gene_ids = NULL,
  first_species = "hsapiens",
  second_species = "mmusculus",
  host = NULL,
  trymart = "ENSEMBL_MART_ENSEMBL",
  archive = TRUE,
  default_hosts = c("useast.ensembl.org", "uswest.ensembl.org", "www.ensembl.org",
    "asia.ensembl.org"),
  year = NULL,
  month = NULL,
  trydataset = NULL,
  attributes = "ensembl_gene_id"
)

Arguments

gene_ids	List of gene IDs to translate.
first_species	Linnean species name for one species.
second_species	Linnean species name for the second species.
host	Ensembl server to query.
trymart	Assumed mart name to use.
archive	Use an archive server?
default_hosts	Set of default hosts to query.
year	When using an archive server, use this year (otherwise it will choose last year).
month	When using an archive server, use this month (otherwise, this month).
trydataset	Choose a dataset to query.
attributes	Key to query

Details

Tested in test_40ann_biomart.R As with my other biomart functions, this one grew out of frustrations when attempting to work with the incredibly unforgiving biomart service. It does not attempt to guarantee a useful biomart connection, but will hopefully point out potentially correct marts and attributes to use for a successful query. I can say with confidence that it works well between mice and humans.

Value

list of 4 elements: The first is the set of all ids, as getLDS seems to always send them all; the second is the subset corresponding to the actual ids of interest, and the 3rd/4th are other, optional ids from other datasets.

See Also

[biomaRt::getLDS()]

Examples

 mouse_yeast_orthologs <- load_biomart_orthologs(gene_ids = NULL, first_species = "mmusculus",
                                                 second_species = "scerevisiae")
 head(mouse_yeast_orthologs$all_linked_genes)

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