buildCorMatrix: Internal function - builds the correlation matrix between an...

In jmarlab/attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

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)

jmarlab/attract documentation built on May 23, 2019, 9:02 p.m.