Nothing
multi.snp.test <-
function(y, x, x.adj = NULL,
type = c("gaussian", "binomial")) {
switch (type,
gaussian = test <- "F",
binomial = test <- "Chisq")
not.adjusted <- FALSE
if (all(is.null(x.adj))) {
not.adjusted <- TRUE
}
if (not.adjusted) {
# no covariates (only intercept)
fit.glm0 <- glm(y ~ 1, family = type)
fit.glm1 <- glm(y ~ ., data = as.data.frame(x), family = type)
aov.glm <- anova(fit.glm0, fit.glm1, test = test)
} else {
# covariates
if (!is.data.frame (x.adj))
x.adj <- as.data.frame (x.adj, stringsAsFactors = FALSE)
if (nrow(x) != nrow(x.adj)) {
stop (paste("Don't match nrow(x) = ",
nrow(x),
" and nrow(x.adj) = ",
nrow(x.adj),
collapse = ""))
}
x.all <- cbind (x, x.adj)
fit.glm0 <- glm (y ~ ., data = x.adj, family = type)
fit.glm1 <- glm (y ~ ., data = x.all, family = type)
aov.glm <- anova (fit.glm0, fit.glm1, test = test)
}
return(list(fit.glm0 = fit.glm0,
fit.glm1 = fit.glm1,
aov.glm = aov.glm,
beta = coef(summary(fit.glm1))))
}
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