Nothing
residualsFAMT <-
function (data, x = 1, test = x, pvalues = NULL) {
if (class(data)[1] != "FAMTdata")
stop("Class of data should be FAMTdata")
nbcovar = ncol(data$covariates)
if (any(!is.element(x, 1:nbcovar)))
stop(paste("x should be a subset of 1:", nbcovar, sep = ""))
if (any(!is.element(test, 1:nbcovar)))
stop(paste("test should be one of ", x, sep = ""))
threshold = 0.05
n = ncol(data$expression)
m = nrow(data$expression)
if (length(pvalues) == 0)
pvalues = raw.pvalues(data, x, test)$pval
SelectH0 = (1:m)[pvalues > threshold]
y = t(data$expression)
xtest = which(is.element(x,test))
covar = data$covariates[, c(x[-xtest], test)]
if (all(data$covariates[, 2] == rep(1, n))) {
P0 = diag(n)
P1 = diag(n) - (1/n) * matrix(1, n, n)
}
if (any(data$covariates[, 2] != rep(1, n))) {
X0 = matrix(rep(1, n), ncol = 1)
if (length(x) > 1)
X0 = model.matrix(y ~ ., data = data.frame(y = rep(1,
n), covar[, -ncol(covar)]))
P0 = diag(n) - X0 %*% solve(t(X0) %*% X0) %*% t(X0)
X1 = model.matrix(y ~ ., data = data.frame(y = rep(1,
n), covar))
P1 = diag(n) - X1 %*% solve(t(X1) %*% X1) %*% t(X1)
}
res = P0 %*% y
res[, -SelectH0] = P1 %*% y[, -SelectH0]
list(residuals = res, SelectH0 = SelectH0, P = P1)
}
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