#' @importFrom limma contrasts.fit lmFit treat
#' @importFrom stats model.matrix
maRank <- function(exprData, classes) {
# should be the same, -1meanA + 1meanC
# design <- model.matrix(~classes+0); contrast <- c(-1, 1);
design <- model.matrix(~classes);
contrast <- c(0, 1);
fit <- lmFit(exprData, design);
# the contrast is the classes difference (0 for intercept, 1 for diff)
fit <- treat(contrasts.fit(fit, contrast));
res <- fit$t;
stopifnot(ncol(res) == 1);
return(res);
}
## voom + limma
## counts a numeric matrix containing raw counts. Counts must be non-negative
## and NAs are not permitted
#' @importFrom limma contrasts.fit lmFit treat voom
#' @importFrom stats model.matrix
rnaRank <- function(exprData, classes) {
# should be the same, -1meanA + 1meanC
# design <- model.matrix(~classes+0); contrast <- c(-1, 1);
## it is doing -1cond[[1]] + cond[[2]]
design <- model.matrix(~classes);
contrast <- c(0, 1);
newExpr <- voom(exprData, design);
fit <- lmFit(newExpr, design);
# the contrast is the classes difference (0 for intercept, 1 for diff)
fit <- treat(contrasts.fit(fit, contrast));
res <- fit$t;
stopifnot(ncol(res) == 1);
return(res);
}
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