## ----preamble,warning=F------------------------------------------------------- library(lfa) library(gcatest) dim(sim_geno) length(sim_trait) ## ----lfa---------------------------------------------------------------------- LF <- lfa(sim_geno, 3) dim(LF) ## ----gcat--------------------------------------------------------------------- gcat_p <- gcat(sim_geno, LF, sim_trait) ## ----gcat2-------------------------------------------------------------------- gcat_p[1:5] ## ----fig1, fig.height=3------------------------------------------------------- library(ggplot2) dat <- data.frame(p = gcat_p[6:10000]) ggplot(dat, aes(p, after_stat(density))) + geom_histogram(binwidth=1/20) + theme_bw()