FindGenes: Investigates whether genes are differential expressed in...

In IntClust: Integrated Data Analysis via Clustering

Description

Due to the shifting of compounds over the clusters for the different methods, it is possible that the same gene is found significant for a different cluster in another method. These can be tracked with the FindGenes function. Per method and per cluster, it will take note of the genes found significant and investigate if these were also find for another cluster in another method.

Usage

FindGenes(DataLimma, names = NULL)

Arguments

DataLimma	Preferably an output of the DiffGenes function. If not, an ID element of the top genes must be present for each cluster of each method specified in the data structure.
names	Optional. Names of the methods.

Value

The returned value is a list with an element per cluster and per cluster one for every gene. Per gene, a vector is given which contain the methods for which the gene was found. If the cluster is changed compared to the reference method of DataLimma, this is indicated with an underscore.

Author(s)

Marijke Van Moerbeke

Examples

data(fingerprintMat)
data(targetMat)
data(geneMat)

MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)

MCF7_DiffGenes_FandT10=DiffGenes(list(MCF7_F,MCF7_T),Selection=NULL,GeneExpr=geneMat,
nrclusters=7,method="limma",sign=0.05,top=10,fusionsLog = TRUE, WeightClust = TRUE, 
names = NULL)

MCF7_SharedGenes=FindGenes(DataLimma=MCF7_DiffGenes_FandT10,names=c("FP","TP"))

IntClust documentation built on May 2, 2019, 5:23 p.m.