extracat (version 1.6-3)

getIs: ME reordering for biclust objects.

Description

Basically this is an auxiliary function used by heattile: It extracts the cluster indices from a biclust object and optimizes the order of the rows and columns in the data matrix with respect to these clusters. Uses the Measure of Effectiveness as an optimization criterion. See ME and optME.

Usage

getIs(biclust, dim, nstart = 20, solver = "nn", adjust.dist = TRUE)

Arguments

biclust

The biclust object.

dim

The dimension of the matrix.

nstart

Number of starting points for the TSP solver in optME.

solver

The TSP solver to use with optME: See solve_TSP.

adjust.dist

If TRUE the ME values used as a distance matrix for the TSP are slightly adjusted by adding a the hamming distance divided by a constant. This keeps identical cases together and also preserves the orders within such groups.

Value

• The cluster indices with respect to the optimized row and column orders in form of a list. The optimized orders for the data matrix are attached as an attribute attr(x, "orders").

Details

The algorithm first computes an indicator matrix for each cluster and then combines these matrices to a 3D table. Then for the first and the second dimension the category orders are optimized with respect to ME. The optimization is done via optME which uses a TSP solver.

See Also

heattile, getIs2