attract (version 1.24.0)

buildCorMatrix: Internal function - builds the correlation matrix between an average transcriptional module expression profile and a set of other genes.

Description

Internal function - builds the correlation matrix between an average transcriptional module expression profile and a set of other genes.

Usage

buildCorMatrix(dat.fr, module.genes, cor.cutoff)

Arguments

dat.fr

a matrix object of gene expression values.

module.genes

character vector specifying genes that belong in this pathway module.

cor.cutoff

numeric value specifying the correlation cut-off.

Value

A character vector of genes that meet the correlation cut-off.

Details

This function is called internally by findCorrPartners which is easier for the user to call since findCorrPartners uses the SynExpressionSet and ExpressionSet class objects directly.

Examples

## Not run: 
# data(subset.loring.eset)
# attractor.states <- findAttractors(subset.loring.eset, "celltype", nperm=10, annotation="illuminaHumanv1.db")
# remove.these.genes <- removeFlatGenes(subset.loring.eset, "celltype", contrasts=NULL, limma.cutoff=0.05)
# mapk.syn <- findSynexprs("04010", attractor.states, remove.these.genes)
# cormat <- buildCorMatrix(exprs(subset.loring.eset), mapk.syn, 0.95)
# ## End(Not run)