This functions retrieves details about the assembly of a queried species.
Usage
get_assemblies(
species_name = "homo_sapiens",
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE
)Arguments
- species_name
The species name, i.e., the scientific name, all letters lowercase and space replaced by underscore. Examples:
'homo_sapiens'(human),'ovis_aries'(Domestic sheep) or'capra_hircus'(Goat).- verbose
Whether to be chatty.
- warnings
Whether to print warnings.
- progress_bar
Whether to show a progress bar.
Value
A tibble, each row being a toplevel sequence,
of 4 variables:
species_nameEnsembl 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'.assembly_nameAssembly name.
assembly_dateAssembly date.
genebuild_methodAnnotation method.
golden_path_lengthGolden path length.
genebuild_initial_release_dateGenebuild release date.
default_coord_system_versionDefault coordinate system version.
assembly_accessionAssembly accession.
genebuild_start_dateGenebuild start date.
genebuild_last_geneset_updateGenebuild last geneset update.
Examples
# Get details about the human assembly
get_assemblies()
#> # A tibble: 1 × 10
#> species_name assembly_name assembly_date genebuild_method golden_path_length
#> <chr> <chr> <chr> <chr> <dbl>
#> 1 homo_sapiens GRCh38.p14 2013-12 full_genebuild 3099750718
#> # ℹ 5 more variables: genebuild_initial_release_date <chr>,
#> # default_coord_system_version <chr>, assembly_accession <chr>,
#> # genebuild_start_date <chr>, genebuild_last_geneset_update <chr>
# Get details about the Mouse and the Fruit Fly genomes
get_assemblies(c('mus_musculus', 'drosophila_melanogaster'))
#> # A tibble: 2 × 10
#> species_name assembly_name assembly_date genebuild_method golden_path_length
#> <chr> <chr> <chr> <chr> <dbl>
#> 1 mus_musculus GRCm39 2020-06 full_genebuild 2728222451
#> 2 drosophila_me… BDGP6.46 NA import 143726002
#> # ℹ 5 more variables: default_coord_system_version <chr>,
#> # assembly_accession <chr>, genebuild_start_date <chr>,
#> # genebuild_last_geneset_update <chr>, genebuild_initial_release_date <chr>