get_toplevel_sequence_info: Get toplevel sequences details

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

Get toplevel sequences details

Description

This function retrieves a few extra details about a toplevel sequence. 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_sequence_info(
  species_name = "homo_sapiens",
  toplevel_sequence = c(1:22, "X", "Y", "MT"),
  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).
toplevel_sequence	A toplevel sequence name, e.g. chromosome names such as "1", "X", or "Y", or a non-chromosome sequence, e.g., a scaffold such as "KI270757.1".
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 8 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'.

toplevel_sequence

Name of the toplevel sequence.

is_chromosome

A logical indicating whether the toplevel sequence is a chromosome (TRUE) or not (FALSE).

coord_system

Coordinate system type.

assembly_exception_type

Coordinate system type.

is_circular

A logical indicating whether the toplevel sequence is a circular sequence (TRUE) or not (FALSE).

assembly_name

Assembly name.

length

Genomic length toplevel sequence in base pairs.

See Also

get_toplevel_sequences()

Examples

# Get details about human chromosomes (default)
get_toplevel_sequence_info()

# Get details about a scaffold
# (To find available toplevel sequences to query use the function
# `get_toplevel_sequences()`)
get_toplevel_sequence_info(species_name = 'homo_sapiens', toplevel_sequence = 'KI270757.1')

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