geneRxCluster: Differential Clustering of Integration Sites

In geneRxCluster: gRx Differential Clustering

Description

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.

geneRxCluster documentation built on Nov. 8, 2020, 4:56 p.m.