readBiclusterResults: Import bicluster results from plain text files

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

Description

This function complements the functionality of writeBiclusterResults in the biclust package. It constructs a Biclust object from a plain text file.

Usage

readBiclusterResults(filename, featureNames, sampleNames, delimiter = ";", ...)

Arguments

filename	Character, name of the file storing biclustering information
featureNames	Optional character vector, feature names of the underlying expression dataset. See details.
sampleNames	Optional character vector, sample names of the underlying expression dataset. See details.
delimiter	Character used to separate features, samples and counts of them.
...	Other parameters passed to the readLines function.

Details

Currently output files written by the writeBiclusterResults function does not contain original feature names or sample names in the expression dataset from which biclusters were mined. The featureNames and sampleNames allow to use this information to construct a Biclust object that has the same dimension as the original expression dataset.

Value

A Biclust object

Author(s)

Jitao David Zhang <[e-mail]>

See Also

In case several biclustering algorithms were applied to the same expression dataset, they can be combined with combineBiclusts once the results were read from plain texts.

Examples

temp <- tempfile()
library(biclust)
data(BicatYeast, package="biclust")
res <- biclust(BicatYeast, method=BCBimax(), number=5)
writeBiclusterResults(temp, res,"CC with delta 1.5",dimnames(BicatYeast)[[1]],dimnames(BicatYeast)[[2]], delimiter=";")
res.back <- readBiclusterResults(temp, delimiter=";")
res.full.back <- readBiclusterResults(temp,featureNames=rownames(BicatYeast), sampleNames=colnames(BicatYeast),delimiter=";")

Example output

Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
Loading required package: lattice

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