############
# QTL_pval #
############
# function to get the QTL decomposed genetic effect for the cross-specific
# parental and ancestral linear models.
QTL_pval <- function(mppData, model, Q.eff, x) {
coeffs <- coef(model)
index <- which(substr(names(coeffs), 1, 3) == "QTL")
coeffs <- coeffs[index]
var.comp <- sqrt(diag(vcov(model)))
index <- which(substr(names(var.comp), 1, 3) == "QTL")
var.comp <- var.comp[index]
var.comp.full <- rep(NA, length(coeffs))
var.comp.full[match(names(var.comp), names(coeffs))] <- var.comp
pval <- 2 * pt(q = abs(coeffs/var.comp.full),
df = df.residual(model), lower.tail = FALSE)
pval <- pval * sign(coeffs)
names(pval) <- substr(names(pval), 4, nchar(names(pval)))
if (Q.eff == "cr") {
pval <- pval[paste0("Cr", unique(mppData$cross.ind))]
} else if (Q.eff == "par") {
pval <- pval[mppData$parents]
} else if (Q.eff == "anc") {
ref.all <- paste0("A.allele", mppData$par.clu[x, ])
pval <- pval[ref.all]
}
return(pval)
}
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