Nothing

```
# Copyright 2012-2013 Paolo Martini <paolo.martini@unipd.it>
#
#
# This file is part of clipper.
#
# clipper is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License
# version 3 as published by the Free Software Foundation.
#
# clipper 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public
# License along with clipper. If not, see <http://www.gnu.org/licenses/>.
hotePaired <- function(exp1, exp2, cliques, performPerm=FALSE, alwaysShrink=FALSE) {
exp1.num <- nrow(exp1)
exp.diff <- exp1 - exp2
if (performPerm) {
signs <- matrix(sample(c(1,-1), exp1.num * NCOL(exp1), replace=TRUE),
nrow=exp1.num)
exp.diff <- exp.diff * signs
}
exp.bar <- colMeans(exp.diff)
maxcliques <- max(sapply(cliques, length))
shrink <- exp1.num < maxcliques || alwaysShrink
exp.s <- estimateExprCov(exp.diff, shrink)
exp.s <- qpIPF(exp.s, cliques)
t2 <- exp1.num * (t(exp.bar) %*% solve(exp.s) %*% exp.bar)
if (length(t2) == 1) {
t2 <- as.numeric(t2)
} else {
warning("t2 longer than one.")
}
p <- ncol(exp1)
np <- exp1.num - p
t2 * np / (p * (exp1.num-1))
}
```

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