In AparicioJohan/GS: Genomic Prediction

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#"
)

Marker based heritability calculation

 library(tidyverse)
 library(GS)
 library(sommer)
 data(DT_cpdata)

 geno <- GT_cpdata
 samp <- rownames(GT_cpdata)
 phen <- DT_cpdata

 tmp <- herMarker(geno, samp, phen, method = c("RKHS","sommer"), traits=c("color","Yield"))

 names(tmp$data)

 tmp$data[,-c(4,5)] %>% spread(method,h)

 tmp$data %>%
   ggplot(aes(x=method, y=h,fill=method, label=round(h,2)))+
   geom_bar(stat = "identity", position = "dodge" )+
   theme_bw()+
   theme(axis.text.x = element_text(hjust = 1,angle = 75))+
   geom_text(aes(method), size=3,nudge_y = 0.08)+
   facet_wrap(~trait,ncol = 2,scales = "free_x")