BiclusterStrategy-class: Class "BiclusterStrategy" for biclusters

In jonalim/mfBiclust: Pipelines for Bi-Clustering Using Matrix Factorization

Description

This class encapsulates bicluster results created by a call to addStrat().

Usage

## S4 method for signature 'BiclusterStrategy'
bcNames(bcs, allBc = FALSE)

## S4 method for signature 'BiclusterStrategy'
featureFactor(bcs, allBc = FALSE)

## S4 method for signature 'BiclusterStrategy'
featureThresh(bcs, allBc = FALSE)

## S4 method for signature 'BiclusterStrategy'
sampleThresh(bcs, allBc = FALSE)

## S4 method for signature 'BiclusterStrategy'
method(bcs)

## S4 method for signature 'BiclusterStrategy'
name(bcs)

## S4 method for signature 'BiclusterStrategy'
nclust(bcs, allBc = FALSE)

## S4 method for signature 'BiclusterStrategy'
sampleFactor(bcs, allBc = FALSE)

## S4 method for signature 'BiclusterStrategy'
threshAlgo(bcs)

Arguments

bcs	A BiclusterSrategy class
allBc	Return data on all stored biclusters

Methods (by generic)

• bcNames: The names of biclusters in the BiclusterStrategy

• featureFactor: Retrieves bcs@factors@fit@W, the matrix factor mapping features to biclusters

• featureThresh: Retrieves bcs@featureThresh, the threshold(s) used to determine each bicluster's feature membership

• sampleThresh: Retrieves bcs@sampleThresh, the threshold(s) used to determine each bicluster's sample membership

• method: Retrieves bcs@factors@method, the biclustering algorithm used to produce bcs

• name: Gets a display-friendly name of a BiclusterStrategy that includes its biclustering algorithm, its thresholding algorithm, and the number of biclusters.

• nclust: Number of clusters in a BiclusterStrategy

• sampleFactor: Retrieves bcs@factors@fit@H, the matrix factor mapping samples to biclusters

• threshAlgo: The algorithm used to calculate biclustering thresholds

Slots

factors

a NMFfit-class or genericFit-class containing a pair of matrices L_{m,k} and R_{k,n}.

featureThresh

a vector of thresholds of length k

sampleThresh

a vector of thresholds of length k

threshAlgo

the name of the thresholding algorithm, or "user"

biclust

a Biclust-class object containing logical bicluster membership matrices and other information

k

the number of biclusters to access when allBc = FALSE.

name

a display friendly character string describing the object

The k slot

The numbers of biclusters requested in the call to addStrat() is stored in BiclusterStrategy@k. A BiclusterStrategy-class object may store more than k biclusters, but accessors only return data on the first k biclusters by default. To obtain data on all stored biclusters, accessors must be called with allBc = TRUE.

See Also

getStrat

jonalim/mfBiclust documentation built on May 4, 2019, 4:13 a.m.