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### modt.R (2015-03-21)
###
### Moderated t Statistic
###
### Copyright 2006-2015 Rainer Opgen-Rhein and Korbinian Strimmer
###
###
### This file is part of the `st' library for R and related languages.
### It is made available under the terms of the GNU General Public
### License, version 3, or at your option, any later version,
### incorporated herein by reference.
###
### This program is distributed in the hope that it will be
### useful, but WITHOUT ANY WARRANTY; without even the implied
### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
### PURPOSE. See the GNU General Public License for more
### details.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
### MA 02111-1307, USA
# Note: these functions require the "limma" library
modt.stat = function (X, L)
{
FUN = modt.fun(L=L)
score = FUN(X)
return( score )
}
modt.fun <- function (L)
{
if (missing(L)) stop("Class labels are missing!")
L = factor(L)
cl = levels(L)
if (length(cl) != 2) stop("Class labels must be specified for two groups, not more or less!")
function(X)
{
L = as.integer(L)
d <- cbind(rep(1, length(L)), L)
fit <- limma::lmFit(t(X), design=d)
eb.out <- limma::eBayes(fit)
modt <- -eb.out$t[,2]
return(modt)
}
}
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