get_biclusters: Extract biclusters from different algorithms/packages

In tdrose/mosbi: Molecular Signature identification using Biclustering

Extract biclusters from different algorithms/packages

Description

Converts biclusters output of different algorithms/packages in to lists of bicluster objects. Many algoritms can be directly executed using the run_... methods from this package. This directly returns the converted results. Not all algorithms are shipped with this package, like Bi-Force, which is running in Java as a standalone tool or BicARE, which required an full import using library(BicARE) in order to run. But their results can be converted using this function.

Usage

get_biclusters(bics, mat, method, transposed = FALSE, filterfun = NULL, ...)

Arguments

bics	A resulting object from a biclustering algorithm (extracted biclusters for fabia) or filename for stored biclustering results.
mat	Original matrix, that was used for biclustering.
method	Used biclustering package. One of "biclust" (can be further specified as "biclust-bimax", "biclust-cc", "biclust-plaid", "biclust-quest", "biclust-qubic", "biclust-spectral", "biclust-xmotifs", "biclust-unibic"), "BicARE", "isa", "fabia", "biforce", "biclustpy", "qubic2" or "akmbiclust".
transposed	Indicate, whether a transposed version of the matrix is used for biclustering. The matrix should not be transposed, when this argument is set to True.
filterfun	A function to filter biclusters. Only if the function returns True, the bicluster is added to the returned list. The function has to accept a bicluster (given as submatrix of mat) filterfun(bicluster_matrix, ...).
...	Other parameters forwarded to the filterfun.

Value

A list of bicluster objects, which are valid (See validate_bicluster).

Examples

m <- matrix(seq(1:16), nrow=4)
# m <- matrix(rnorm(10000), nrow=100)
# res <- isa2::isa(m)
# get_biclusters(res, m, "isa")

tdrose/mosbi documentation built on May 4, 2022, 3:22 p.m.