biclustRank-package: Ranking of Biclusters

In biclustRank: Ranking of biclusters using another data source

Description

Ranking of gene expression-based biclusters using another source of information, (e.g. the chemical structure, target predictions, HCS, etc) This allows to further explore whether compounds in a bicluster also share other properties aside from gene expression profiles.

Details

Package:	biclustRank
Type:	Package
Version:	1.0
Date:	2015-01-21
License:	GPL3

~~ An overview of how to use the package, including the most important ~~ ~~ functions ~~

Author(s)

Nolen Joy Perualila

Maintainer:Nolen Joy Perualila<[e-mail]> ~~ The author and/or maintainer of the package ~~

References

soon

See Also

~~ Optional links to other man pages, e.g. ~~ ~~ <pkg> ~~

Examples

##load data
data(expressionMatrix)
data(fingerprints)

##run Fabia
	set.seed(12345)
	resFabia <- fabia(expressionMatrix, p=10, cyc=1000,  alpha=0.1, random=0)
##other options: plaid and isa

##get Fabia biclusters
	bicF <- extractBicList(data=expressionMatrix, biclustRes=resFabia, p=10, bcMethod="fabia")

## get similarity matrix for the fingerprints
fpfDist <- Distance(dataB = t(fingerprints), distmeasure = "tanimoto")
fpfSim <- 1-fpfDist

##extract similarity matrix per bc
simMat <- extractSimBC(biclustList = bicF, simMat = fpfSim, p=10 )

## get lower triangle of simMat
simVecBC <- getLowerSim(simMat)

## cdf plot
cumBC(LstTot=simVecBC, prob=TRUE, refScore=0.6)

##boxplot
boxplotBC(simVecBC=simVecBC,qVal=0.5,rank=TRUE)

##summary statistics table
statTab(simVecBC=simVecBC,ordering=4)

##top N subfeatures used for the calculation of similarity
fpfs <- sapply(1:length(bicF), function(row) choosefp(bicF,fingerprints,bcNum=row,N=100))
colnames(fpfs) <- names(bicF)

bcNum=c(4,6,7)
gComb <- unlist(sapply(bicF, "[[", 2) )
geneSim <-  cor(expressionMatrix[gComb,])^2

## heatmap of similarity scores for selected biclusters
heatmapBC(simMat=geneSim, bicRes=bicF, bcNum = bcNum, main=paste("Transcriptional Profiles Similarity"))
heatmapBC(simMat=fpfSim, bicRes=bicF, bcNum =bcNum, main=paste("Structural Profiles Similarity"))

##profiles plot of genes and heatmap of fingerprints
par(mfrow=c(2,1))
bcNum=6
ppBC(bicF,eMat=expressionMatrix, bcNum=bcNum)
heatmapBC2(fingerprints,bicF,bcNum=bcNum, N=10)

##plot loadings/scores
plotFabia(resFabia, bicF, bcNum=7, plot=2)

biclustRank documentation built on May 2, 2019, 4:54 p.m.