get_cytogenetic_bands: Get cytogenetic bands by species

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

Get cytogenetic bands by species

Description

This function retrieves cytogenetic bands. If no cytogenetic information is available for the queried species then it will be omitted from in the returned value.

Usage

get_cytogenetic_bands(
  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 cytogenetic band, 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'.

assembly_name

Assembly name.

cytogenetic_band

Name of the cytogenetic_band.

chromosome

Chromosome name.

start

Genomic start position of the cytogenetic band. Starts at 1.

end

Genomic end position of the cytogenetic band. End position is included in the band interval.

stain

Giemsa stain results: Giemsa negative, 'gneg'; Giemsa positive, of increasing intensities, 'gpos25', 'gpos50', 'gpos75', and 'gpos100'; centromeric region, 'acen'; heterochromatin, either pericentric or telomeric, 'gvar'; and short arm of acrocentric chromosomes are coded as 'stalk'.

strand

Strand.

Examples

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

# Get toplevel sequences for Mus musculus
get_cytogenetic_bands('mus_musculus')

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