Geneset.intersect: Intersection over resulting gene sets of 'PathwaysIter'...

In IntClust: Integrated Data Analysis via Clustering

Description

The function Geneset.intersect puts per method the results of the PathwaysIter function together for each cluster and takes the intersection over the iterations per cluster per method. This is to see if over the different resamplings of the data, similar pathways were discovered.

Usage

Geneset.intersect(PathwaysOutput, Selection=FALSE, sign=0.05, names = NULL,
seperatetables = FALSE, separatepvals = FALSE)

Arguments

PathwaysOutput	The output of the PathwaysIter function.
Selection	Logical. Indicates whether or not the output of the pathways function were concentrated on a specific selection of compounds. If this was the case, Selection should be put to TRUE. Otherwise, it should be put to FALSE.
sign	The significance level to be handled for cutting of the pathways.
names	Optional. Names of the methods.
seperatetables	Logical. If TRUE, a separate element is created per cluster. containing the pathways for each iteration.
separatepvals	Logical. If TRUE, the p-values of the each iteration of each pathway in the intersection is given. If FALSE, only the mean p-value is provided.

Value

The output is a list with an element per method. For each method, it is portrayed per cluster which pathways belong to the intersection over all iterations and their corresponding mean p-values.

Author(s)

Marijke Van Moerbeke

See Also

PathwaysIter

Examples

## Not run: 
data(fingerprintMat)
data(targetMat)
data(geneMat)
data(GeneInfo)
data(ListGO)

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)

L=list(MCF7_F,MCF7_T)

MCF7_Paths_FandT=PathwaysIter(list(MCF7_F,MCF7_T),GeneExpr=geneMat,nrclusters=7,
method=c("limma", "MLP"),ENTREZID=GeneInfo[,1],geneSetSource = "GOBP",top=NULL,
topG=NULL,GENESET=ListGO,sign=0.05,niter=2,fusionsLog=TRUE,WeightClust=TRUE,
names=c("FP","TP"))

MCF7_Paths_intersection=Geneset.intersect(MCF7_Paths_FandT,0.05,names=c("FP",
"TP"),seperatetables=FALSE,separatepvals=FALSE)

str(MCF7_Paths_intersection)

## End(Not run)

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