## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(SEAGLE) ## ----------------------------------------------------------------------------- acr_loc <- system.file("extdata", "ACR.raw", package = "SEAGLE") acr <- read.delim(acr_loc, sep=" ") ## ----------------------------------------------------------------------------- dim(acr) head(acr) ## ----------------------------------------------------------------------------- G <- as.matrix(acr[,-c(1:6)]) dim(G) ## ----------------------------------------------------------------------------- # Determine number of individuals and loci n <- dim(G)[1] L <- dim(G)[2] # Generate synthetic phenotype and covariate data set.seed(1) y <- 2 * rnorm(n) set.seed(2) X <- rnorm(n) set.seed(3) E <- rnorm(n) ## ----------------------------------------------------------------------------- objSEAGLE <- prep.SEAGLE(y=y, X=X, intercept=0, E=E, G=G) ## ----------------------------------------------------------------------------- res <- SEAGLE(objSEAGLE, init.tau=0.5, init.sigma=0.5) res$T res$pv