breeding_values: Prediction of QTL-based breeding values from REMIM model
In guilherme-pereira/QTLpoly: Random-effect multiple QTL mapping in autopolyploids

Description Usage Arguments Value Author(s) References See Also Examples

Computes breeding values for each genotyped individual based on multiple QTL models

breeding_values(data, fitted)

## S3 method for class 'qtlpoly.bvalues'
plot(x, pheno.col = NULL)

`data`	an object of class `qtlpoly.data`.
`fitted`	an object of class `qtlpoly.fitted`.
`x`	an object of class `qtlpoly.bvalues` to be plotted.
`pheno.col`	a numeric vector with the phenotype column numbers to be plotted; if `NULL`, all phenotypes from `'data'` will be included.

An object of class qtlpoly.bvalues which is a list of results for each trait containing the following components:

`pheno.col`	a phenotype column number.
`y.hat`	a column matrix of breeding value for each individual.

A ggplot2 histogram with the distribution of breeding values.

Guilherme da Silva Pereira, gdasilv@ncsu.edu

Pereira GS, Gemenet DC, Mollinari M, Olukolu BA, Wood JC, Mosquera V, Gruneberg WJ, Khan A, Buell CR, Yencho GC, Zeng ZB (2020) Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population, Genetics 215 (3): 579-595. http://doi.org/10.1534/genetics.120.303080.

read_data, fit_model

  ## Not run: 
  # load raw data
  data(maps)
  data(pheno)

  # estimate conditional probabilities using mappoly package
  library(mappoly)
  genoprob <- lapply(maps, calc_genoprob)

  # prepare data
  data <- read_data(ploidy = 6, geno.prob = genoprob, pheno = pheno, step = 1)

  # perform remim
  remim.mod <- remim(data = data, w.size = 15, sig.fwd = 0.01, sig.bwd = 0.0001,
    d.sint = 1.5, n.clusters = 4, plot = "remim")

  # fit model
  fitted.mod <- fit_model(data = data, model = remim.mod, probs = "joint", 
    polygenes = "none")

  # predict genotypic values
  y.hat <- breeding_values(data = data, fitted = fitted.mod)
  plot(y.hat)
  
## End(Not run)