maizeG: Maize Genomic Relationship Matrix (GRM)

In allogamous/EnvRtype: Envirotyping Tools for Crop Research and Genetic Improvment

Maize Genomic Relationship Matrix (GRM)

Description

This data set was included in Souza et al. (2017) and Cuevas et al (2019) is from the Helix Seeds Company (HEL). Genotyping Array of 616 K SNPs (Single Nucleotide Polymorphism) (Unterseer et al. 2014). Standard quality controls (QC) were applied to the data, removing markers with a Call Rate $ 0.95. The remaining missing data in the lines were imputed with the Synbreed package (Wimmer et al. 2015) using the algorithms from the Beagle 4.0 software (Browning and Browning 2009). Markers with Minor Allele Frequency (MAF) of # 0.05 were removed. After applying QC, 52,811 SNPs were available to make the predictions. The phenotypic and genomic data of inbred lines are credited to Helix Seeds Ltda. Company.

Usage

data(maizeG)

Format

An object of class matrix (inherits from array) with 150 rows and 150 columns.

Examples

data(maizeG)

allogamous/EnvRtype documentation built on Nov. 1, 2024, 3:48 a.m.