rqubic (version 1.18.0)

features-methods: Extract features and conditions

Description

Generic function features and conditions, as well as auxillary count functions, are implemented for Biclust objects.

They can be used in one of the following forms:

1. Used on a Biclust, and without specifying index, features or conditions returns the unique and ordered features or conditions involved in at least one bicluster, and featureCount or conditionCount returns the length of repsective vectors. To get the feature/condition numbers in each bicluster of the set, use BCfeatureCount/BCconditionCount.
2. Used on a Biclust and provided index (indices), the features/conditions or their counts are returned for specified biclusters.

In addition, featureNames and sampleNames are of the same implementation as features and conditions.

Methods

signature(object = "QUBICBicluster")

Information about all the biclusters.

signature(object = "Biclust", index = "missing")

Information about all the biclusters in the set.

signature(object = "Biclust", index = "ANY")

Information about selected biclusters in the set, the index can be integers or logical variables for subsetting.

References

Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paternson and Ying Xu (2009) QUBIC: a qualitative biclustering algorithm for analyses of gene expression data. Nucleic Acids Research, 37:e101

See Also

See other methods implemented for the Biclust class in the biclust package. And the methods specific for QUBICBiclusterSet.

Examples

library(Biobase)
library(biclust)
example.file <- system.file("extdata", "sampleExpressionSet.blocks", package="rqubic")

example.block <- parseQubicBlocks(example.file)

head(features(example.block))
featureCount(example.block)
head(conditions(example.block))
conditionCount(example.block)

BCfeatureCount(example.block)
BCfeatures(example.block)[1:2]
BCconditionCount(example.block)
BCconditions(example.block)[1:2]

head(featureNames(example.block))
head(sampleNames(example.block))