infergen

Infer additive and dominance genotypes of hybrids based on their parental genotypes.

Performs genomic prediction of hybrid performance using eight statistical methods including GBLUP, BayesB, RKHS, PLS, LASSO, EN, LightGBM and XGBoost along with additive and additive-dominance models. Users are able to incorporate parental phenotypic information in all methods based on their specific needs. (Xu S et al(2017) <doi:10.1534/g3.116.038059>; Xu Y et al (2021) <doi: 10.1111/pbi.13458>).

Yang Xu

predhy

Genomic Prediction of Hybrid Performance

Guangning Yu

Yanru Cui

Shizhong Xu

Chenwu Xu

infergen function

<dl><dt>inbred_gen</dt>
<dd>a matrix for genotypes of parental lines in numeric format, coded as 1, 0 and -1. The row.names of inbred_gen must be provied. It can be obtained from the original genotype using <code>convertgen</code> function.</dd>
<dt>hybrid_phe</dt>
<dd>a data frame with three columns. The first column and the second column are the names of male and female parents of the corresponding hybrids, respectively; the third column is the phenotypic values of hybrids.
The names of male and female parents must match the rownames of inbred_gen. Missing (NA) values are not allowed.</dd></dl>

Arguments

Infer Genotype of Hybrids — infergen

<dl>

<dt>inbred_gen</dt>
<dd>a matrix for genotypes of parental lines in numeric format, coded as 1, 0 and -1. The row.names of inbred_gen must be provied. It can be obtained from the original genotype using <code>convertgen</code> function.</dd>


<dt>hybrid_phe</dt>
<dd>a data frame with three columns. The first column and the second column are the names of male and female parents of the corresponding hybrids, respectively; the third column is the phenotypic values of hybrids.
The names of male and female parents must match the rownames of inbred_gen. Missing (NA) values are not allowed.</dd>

</dl>

infergen: Infer Genotype of Hybrids

Description

Usage

Value

Arguments

Examples