BiclusterExperiment-class: Class "BiclusterExperiment" for data and biclusters

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

Description

This class encapsulates data for one or more biclustering runs derived from the same abundance data. Objects can be created using the BiclusterExperiment constructor. A subclass of eSet.

Usage

## S4 method for signature 'matrix'
BiclusterExperiment(m, bcs = list(),
  phenoData = Biobase::annotatedDataFrameFrom(m, byrow = FALSE),
  featureData = annotatedDataFrameFrom(m, byrow = TRUE), pp = FALSE,
  maxNa = 0)

## S4 method for signature 'ANY'
BiclusterExperiment(m, bcs = list(),
  phenoData = Biobase::annotatedDataFrameFrom(m, byrow = FALSE),
  featureData = annotatedDataFrameFrom(m, byrow = TRUE), pp = FALSE,
  maxNa = 0)

## S4 method for signature 'BiclusterExperiment'
as.matrix(x)

## S4 method for signature 'BiclusterExperiment'
names(x)

## S4 method for signature 'BiclusterExperiment'
strategies(x)

Arguments

m	The data on which derived BiclusterStrategy objects will be calculated. Should be a matrix or a class coercible to matrix, with samples as columns and features as rows
bcs	May be a list of BiclusterStrategy objects that have been computed from m previously
phenoData	Metadata about the rows of m
featureData	Metadata about the columns of m
pp	Whether to preprocess m by removing rows and columns with excessive missing data
maxNa	If pp, rows and columns with over maxNa elements missing are discarded
x	A BiclusterExperiment-class object

Methods (by generic)

• BiclusterExperiment: Default constructor method

• BiclusterExperiment: Attempts to coerce m to a matrix before encapsulating it in a BiclusterExperiment

• names: Retrieves the names of any encapsulated BiclusterStrategy-class objects.

• strategies: Get/set a list of the BiclusterStrategy objects contained by this BiclusterExperiment.

Slots

assayData

Object of class AssayData-class in the "list" storage mode. AssayData must have a matrix named "abund" with rows representing features and columns representing samples. Any other matrices in assayData are ignored by this package.

strategies

A list of BiclusterStrategy-class objects

phenoData

See eSet-class.

featureData

eSet-class.

experimentData

eSet-class. Not accessed by any functions in mfBiclust.

annotation

eSet-class. Not accessed by any functions in mfBiclust.

protocolData

eSet-class. Not accessed by any functions in mfBiclust.

See Also

eSet-class

getStrat

Examples

bce <- BiclusterExperiment(yeast_benchmark[[1]])

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