This function retrieves variant sources, i.e. a list of databases used by Ensembl from which variant information is retrieved.
get_variation_sources( species_name = "human", verbose = FALSE, warnings = TRUE, progress_bar = TRUE )
| species_name | The species name, i.e., the scientific name, all letters
lowercase and space replaced by underscore. Examples: |
|---|---|
| verbose | Whether to be chatty. |
| warnings | Whether to print warnings. |
| progress_bar | Whether to show a progress bar. |
A tibble, each row being a variant database,
of 8 variables:
Ensembl species name: this is the name used internally
by Ensembl to uniquely identify a species by name. It is the scientific
name but formatted without capitalisation and spacing converted with an
underscore, e.g., 'homo_sapiens'.
Database name.
Database type, e.g., chip (genotyping chip) or lsdb
(locus-specific database).
Database version.
Somatic status.
Database description.
Database's URL.
Data types to be found at database.
get_variation_sources makes GET requests to
info/variation/:species.
# Retrieve variant sources for human (default) get_variation_sources()#> # A tibble: 36 × 8 #> species_name db_name type version somatic_status description url #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 human dbSNP NA 154 mixed Variants (inclu… http://… #> 2 human Archive … NA 154 mixed Former dbSNP va… http://… #> 3 human dbSNP HG… NA 154 mixed HGVS annotation… http://… #> 4 human Former d… NA 154 mixed Former dbSNP va… http://… #> 5 human PharmGKB NA 05/01/… germline A pharmacogenom… https:/… #> 6 human HGMD-PUB… NA 2020.4 germline Variants from H… http://… #> 7 human DGVa NA 01/2020 mixed Database of Gen… https:/… #> 8 human NHGRI-EB… NA 15/12/… germline Variants associ… https:/… #> 9 human EGA NA 01/2021 germline Variants import… https:/… #> 10 human UniProt NA 05/01/… mixed Variants with p… http://… #> # … with 26 more rows, and 1 more variable: data_types <list># Retrieve variant sources for mouse get_variation_sources(species_name = 'mus_musculus')#> # A tibble: 5 × 8 #> species_name db_name type version somatic_status description url data_types #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <list> #> 1 mus_musculus dbSNP NA 150 mixed Variants (… http… <chr [1]> #> 2 mus_musculus Archiv… NA 150 mixed Former var… http… <chr [1]> #> 3 mus_musculus DGVa NA 05/2018 mixed Database o… http… <chr [2]> #> 4 mus_musculus IMPC NA 17/12/… germline Internatio… http… <chr [1]> #> 5 mus_musculus MGI NA 17/12/… germline Mouse Geno… http… <chr [1]>