################
# QTLModelQeff #
################
# computation of the model for the QTL genetic effects
# arguments
# mppData : data object
# Q.list: list of QTL positions
# VCOV: variance covariance structure
# trait: trait values
# cross.mat : cross intercept incidence matrix
QTLModelQeff <- function(mppData, trait, cross.mat, Q.list, VCOV){
if(VCOV == "h.err"){
n.QTL <- length(Q.list)
formula <- paste("trait ~ -1 + cross.mat + ",
paste(paste0("Q", 1:n.QTL), collapse = "+"))
model <- lm(as.formula(formula), data = Q.list)
} else if ((VCOV == "h.err.as") || (VCOV == "cr.err")) {
# n.QTL <- length(Q.list)
#
# dataset <- data.frame(do.call(cbind, Q.list),
# cr.mat = factor(mppData$cross.ind,
# levels = unique(mppData$cross.ind)),
# trait = trait)
#
# Q.names <- function(x, Q.list){
# paste0("Q", x, attr(Q.list[[x]], "dimnames")[[2]])
# }
#
# names.QTL <- unlist(lapply(X = 1:n.QTL, FUN = Q.names, Q.list = Q.list))
# names.QTL <- make.names(names.QTL)
#
# colnames(dataset)[1:length(names.QTL)] <- names.QTL
#
# fbegin <- "trait ~ -1 + cr.mat +"
#
# formula <- paste(fbegin, paste(names.QTL, collapse = "+"))
#
# if(VCOV == "h.err.as"){ formula.R <- "~idv(units)"
# } else if (VCOV == "cr.err") {formula.R <- "~at(cr.mat):units"}
#
# model <- asreml::asreml(fixed = as.formula(formula), rcov = as.formula(formula.R),
# data = dataset, trace = FALSE, na.method.Y = "omit",
# na.method.X = "omit")
} else if ((VCOV == "pedigree") || (VCOV == "ped_cr.err")) {
# n.QTL <- length(Q.list)
#
# dataset <- data.frame(do.call(cbind, Q.list),
# cr.mat = factor(mppData$cross.ind,
# levels = unique(mppData$cross.ind)),
# trait = trait,
# genotype = mppData$geno.id)
#
# Q.names <- function(x, Q.list){
# paste0("Q", x, attr(Q.list[[x]], "dimnames")[[2]])
# }
#
# names.QTL <- unlist(lapply(X = 1:n.QTL, FUN = Q.names, Q.list = Q.list))
# names.QTL <- make.names(names.QTL)
#
# colnames(dataset)[1:length(names.QTL)] <- names.QTL
#
# fbegin <- "trait ~ 1 +"
#
# formula <- paste(fbegin, paste(names.QTL, collapse = "+"))
#
#
# if(VCOV == "pedigree"){ formula.R <- "~idv(units)"
# } else if (VCOV == "ped_cr.err") { formula.R <- "~at(cr.mat):units"}
#
# model <- asreml::asreml(fixed = as.formula(formula), random = ~ ped(genotype),
# rcov = as.formula(formula.R),
# ginverse = list(genotype = ped.mat.inv),
# data = dataset, trace = FALSE, na.method.Y = "omit",
# na.method.X = "omit")
}
return(model)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.