PreparePathway: Preparing a data set for pathway analysis

In IntClust: Integrated Data Analysis via Clustering

Description

The functions for pathway analysis in this package can also work on results of the integrated data functions. However, a differential gene expression needs to be conducted to perform pathway analysis. The function PreparePathway checks if the necessary elements are present in the data structures and if not, the elements such as p-values are created. It is an internal function to all pathway analysis functions but can be used separately as well.

Usage

PreparePathway(Object, GeneExpr, topG, sign)

Arguments

Object	A list with at least an element with the name "Compounds" such that the function knows which compounds to test for differential gene expression. If the elements "Genes" and "pvalsgenes" are present as well, these will be collected and the gene expression is not analyzed.
GeneExpr	The gene expression matrix or ExpressionSet of the objects. The rows should correspond with the genes.
topG	Overrules sign. The number of top genes to be returned in the result. If not specified, only the significant genes are shown.
sign	The significance level to be handled.

Value

The returned value is a list with three elements:

pvalsgenses	This is a list with that contains a vector of raw p-values for every group of tested compounds.
Compounds	This is a list with that contains another list per group of tested compounds. Every list contains the lead compounds and the ordered compounds.
Genes	This is a list with that contains contains another list per group of tested compounds. Every list contains two data frames, one with information on the top genes and one with information on all genes.

Author(s)

Marijke Van Moerbeke

Examples

data(fingerprintMat)
data(geneMat)

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


L1=list(MCF7_F)

Comps1=FindCluster(L1,nrclusters=7,select=c(1,1))
Comps2=FindCluster(L1,nrclusters=7,select=c(1,2))
Comps3=FindCluster(L1,nrclusters=7,select=c(1,3))


L2=list()

L2$'Cluster 1'$Compounds$LeadCpds=Comps1
L2$'Cluster 2'$Compounds$LeadCpds=Comps2
L2$'Cluster 3'$Compounds$LeadCpds=Comps2

MCF7_PreparePaths=PreparePathway(Object=L2,GeneExpr=geneMat,topG=NULL,sign=0.05)
str(MCF7_PreparePaths)

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