geneRxCluster provides the function
gRxCluster and friends.
Details
Windows defined by k consecutive integration sites
are scanned. A two class indicator is tallied to determine
whether one class dominates. If one does, a flag is set and
the window is retained. Various values of k are
used. Conflicts between overlapping windows with the same
value of k can occur — two windows are dominated
by the two different classes. In that case, the sites of
overlap are marked and neither window is retained.
Conflicts can also arise between windows differing in their
values of k. In that case, the window having the
smaller value of k is retained and the other is
discarded.
Permutation tests and permutation based false discovery
rates are available.
Filtering of windows is allowed so that regions which are
sparsely populated need not be studied.