get_variantset

Downloads a two-dimensional marker matrix for all samples in the currently 
active variant set, using the efficient Flapjack file format from the server. 
Row names correspond to marker IDs and column names correspond to unique 
sample IDs. Genotype calls are returned in character format.

This R package assists breeders in linking data systems with their analytic pipelines,
a crucial step in digitizing breeding processes. It supports querying and retrieving
phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>,
'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>,
'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls),
, and 'Germinate' <https://germinateplatform.github.io/get-germinate/>.
Extra helper functions support environmental data sources, including
'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO'
'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.

Khaled Al-Shamaa

QBMS

Query the Breeding Management System(s)

Mariano Omar Crimi

Zakaria Kehel

Johan Aparicio

ICARDA 

get_variantset function

Khaled Al-Shamaa (<a href="/link/k.el-shamaa%40cgiar.org?package=QBMS&version=2.0.0" data-mini-rdoc="QBMS::k.el-shamaa@cgiar.org">k.el-shamaa@cgiar.org</a>)

Author

Get Marker Matrix from the Selected Variant Set — get_variantset

Khaled Al-Shamaa (<a href='mailto:k.el-shamaa@cgiar.org'>k.el-shamaa@cgiar.org</a>)

get_variantset: Get Marker Matrix from the Selected Variant Set

Description

Usage

Arguments

Value

Author

See Also