buildCorMatrix {attract} | R Documentation

## 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.

### 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.

### Value

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

### Author(s)

Jessica Mar

### 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)

[Package attract version 1.42.0 Index]