fcFilter {rqubic}R Documentation

Feature-Condition Filter

Description

Filter Biclusters by feature and concition counts. Biclusters with fewer features or conditions than specified thresholds are removed.

Usage

fcFilter(object, ...)

Arguments

object

A Biclust object

...

Two parameters are accepted: feat.min and cond.min. They indicate the minimum number of features (conditions) in biclusters, which are to be accepted. It is allowed to only specify one threshold. If both are specified, only biclusters fulfilling both criterion are accepted.

Value

A Biclust object.

Author(s)

Jitao David Zhang <jitao_david.zhang@roche.com>

Examples

data(sample.ExpressionSet, package="Biobase")
rqubic.example.discret <- quantileDiscretize(sample.ExpressionSet, rank=2L)

rqubic.example.sel.seeds <- generateSeeds(rqubic.example.discret, minColWidth=2L)

rqubic.example.blocks <- quBicluster(rqubic.example.sel.seeds,
    rqubic.example.discret,
    report.no=200L,
    filter.proportion=0.1)

print(rqubic.example.blocks)
print(fcFilter(rqubic.example.blocks,feat.min=10))
print(fcFilter(rqubic.example.blocks,cond.min=2))
print(fcFilter(rqubic.example.blocks,feat.min=10, cond.min=2))
[Package rqubic version 1.33.0 Index]