combineBiclusts-methods: Combine two or more Biclust objects into one

In rqubic: Qualitative biclustering algorithm for expression data analysis in R

Description

Combining two or more Biclust objects into one object. These objects must be of same dimension, namely have same numbers of features and samples, although the numbers of biclusters do not have to be the same (and usually are not).

Methods

signature(x = "Biclust", y = "Biclust")

Method for any Biclust objects

signature(x = "QUBICBiclusterSet", y = "QUBICBiclusterSet")

Method for QUBICBiclusterSet only. Besides combining biclusters, they will also combine parameters and information stored in each QUBICBiclusterSet into the returning object.

signature(x = "list", y = "missing")

Method for a list of Biclust or QUBICBiclusterSet objects.

Examples

data(sample.ExpressionSet, package="Biobase")
re1.discret <- quantileDiscretize(sample.ExpressionSet, rank=1L)
re1.sel.seeds <- generateSeeds(re1.discret, minColWidth=2L)
re1.blocks <- quBicluster(re1.sel.seeds,
    re1.discret,
    report.no=50L,
    filter.proportion=0.1)

re2.discret <- quantileDiscretize(sample.ExpressionSet, rank=2L)
re2.sel.seeds <- generateSeeds(re2.discret, minColWidth=2L)
re2.blocks <- quBicluster(re2.sel.seeds,
    re2.discret,
    report.no=50L,
    filter.proportion=0.1)

re3.discret <- quantileDiscretize(sample.ExpressionSet, rank=3L)
re3.sel.seeds <- generateSeeds(re3.discret, minColWidth=2L)
re3.blocks <- quBicluster(re2.sel.seeds,
    re2.discret,
    report.no=50L,
    filter.proportion=0.1)

re12.blocks <- combineBiclusts(re1.blocks, re2.blocks)
re123.blocks <- combineBiclusts(re1.blocks, re2.blocks, re3.blocks)
re123.list.blocks <- combineBiclusts(list(re1.blocks, re2.blocks,
re3.blocks))
stopifnot(identical(re123.blocks, re123.list.blocks))

rqubic documentation built on Nov. 8, 2020, 8:20 p.m.