predhy.predict_NCII {predhy}

Predict the Performance of Hybrids

Description

Predict all potential crosses of a given set of parents using a subset of crosses as the training sample.

Usage

predhy.predict_NCII(
  inbred_gen,
  hybrid_phe,
  parent_phe = NULL,
  male_name = hybrid_phe[, 1],
  female_name = hybrid_phe[, 2],
  method = "GBLUP",
  model = "A",
  select = "top",
  number = "100"
)

Arguments

inbred_gen

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 convertgen function.

hybrid_phe

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.

parent_phe

a matrix of a phenotypic values of parent.The names parent_phe must match the rownames of inbred_gen. Default is NULL.

male_name

a vector of the names of male parents.

female_name

a vector of the names of female parents.

method

eight GS methods including "GBLUP", "BayesB", "RKHS", "PLS", "LASSO", "EN", "XGBoost", "LightGBM". Users may select one of these methods. Default is "GBLUP".

model

the prediction model. There are two options: model = "A" for the additive model, model = "AD" for the additive-dominance model,model = "A-P" for the additive-phenotypic model,model = "AD-P" for the additive-dominance-phenotypic model. Default is model = "A".

select

the selection of hybrids based on the prediction results. There are three options: select = "all", which selects all potential crosses. select = "top", which selects the top n crosses. select = "bottom", which selects the bottom n crosses. The n is determined by the param number.

number

the number of selected top or bottom hybrids, only when select = "top" or select = "bottom".

Value

a data frame of prediction results with two columns. The first column denotes the names of male and female parents of the predicted hybrids, and the second column denotes the phenotypic values of the predicted hybrids.

Examples

## load example data from hypred package
data(hybrid_phe)
data(input_geno)

## convert original genotype
inbred_gen <- convertgen(input_geno, type = "hmp2")

pred<-predhy.predict_NCII(inbred_gen,hybrid_phe,method="LASSO",model="A")
pred<-predhy.predict_NCII(inbred_gen,hybrid_phe,method="LASSO",model = "AD",select="all")