get_toplevel_sequences: Get toplevel sequences by species

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

Get toplevel sequences by species

Description

This function retrieves toplevel sequences. These sequences correspond to genomic regions in the genome assembly that are not a component of another sequence region. Thus, toplevel sequences will be chromosomes and any unlocalised or unplaced scaffolds.

Usage

get_toplevel_sequences(
  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_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.

toplevel_sequence

Name of the toplevel sequence.

length

Genomic length toplevel sequence in base pairs.

Examples

# Get toplevel sequences for the human genome (default)
get_toplevel_sequences()

# Get toplevel sequences for Caenorhabditis elegans
get_toplevel_sequences('caenorhabditis_elegans')

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