R/geneRxCluster-package.R

In geneRxCluster: gRx Differential Clustering

##' Differential Clustering of Integration Sites
  ##'
  ##' geneRxCluster provides the function \code{\link{gRxCluster}} and friends.
  ##'
  ##' Windows defined by \code{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 \code{k} are used. Conflicts between
  ##' overlapping windows with the same value of \code{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 \code{k}. In that case, the window having the
  ##' smaller value of \code{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.
  ##'
  ##' @docType package
  ##' @name geneRxCluster
  ##' 
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