get_karyotypes: Get the karyotype of a species

In ramiromagno/ensemblr: R Client for the Ensembl REST API

Get the karyotype of a species

Description

This function retrieves the set of chromosomes of a species.

Usage

get_karyotypes(
  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 chromosome, of 4 variables:

species_name

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'.

coord_system

Coordinate system type.

chromosome

Chromosome name.

length

Genomic length of the chromsome in base pairs.

Examples

# Get the karyotype of Caenorhabditis elegans
get_karyotypes('caenorhabditis_elegans')

# Get the karyotype of the Giant panda
get_karyotypes('ailuropoda_melanoleuca')

ramiromagno/ensemblr documentation built on Oct. 19, 2023, 11:12 a.m.