get_smarter_genotypes: Get SMARTER Genotypes

In cnr-ibba/r-smarter-api: Fetch SMARTER Data Through REST API

Get SMARTER Genotypes

Description

Retrieve genotypes data from SMARTER database. Only information about the supported assemblies are returned (see get_smarter_info for more information).

Usage

get_smarter_genotypes(species, assembly, dest_path = NULL)

Arguments

species	a smarter species ("Goat", "Sheep")
assembly	the smarter working assembly for such species
dest_path	the path where the file will be downloaded. If NULL, the file will be downloaded in the current working directory

Value

a character string with the path to the downloaded file is returned

About SMARTER supported assemblies

Currently SMARTER supports OAR3 and OAR4 assemblies for Sheep and CHI1 and ARS1 assemblies for goat. Genotypes are provided in PLINK binary format, and compressed in a zip file.

Examples

## Not run: 
# get genotypes for sheep OAR3 in current directory
get_smarter_genotypes(species = "Sheep", assembly = "OAR3")

## End(Not run)

cnr-ibba/r-smarter-api documentation built on July 2, 2024, 12:24 p.m.