get_biclusters {mosbi} | R Documentation

## 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")

[Package mosbi version 1.0.3 Index]