attract (version 1.24.0)

findCorrPartners: Determines Genes with Highly Correlated Expression Profiles to a Synexpression Group

Description

This function finds genes with expression profiles highly correlated to a synexpression group.

Usage

findCorrPartners(mySynExpressionSet, myEset, removeGenes = NULL, cor.cutoff = 0.85, ...)

Arguments

mySynExpressionSet

SynExpressionSet object.

myEset

ExpressionSet object.

removeGenes

vector of probes that specify those genes who demonstrate little variability across the different celltypes and thus should be removed from downstream analysis.

cor.cutoff

numeric value specifying the correlation cut-off.

...

additional arguments.

Value

A SynExpressionSet object which stores the genes that are highly correlated with the synexpression group provided, and their average expression profile.

Details

Genes with highly correlated profiles to the synexpression groups (e.g. R > 0.85) are also likely to be integral in maintaining cell type-specific differences, however due to their lack of inclusion in resources like KEGG, would not have been picked up by the first GSEA step using findAttractors.

Examples

data(subset.loring.eset)
attractor.states <- findAttractors(subset.loring.eset, "celltype", 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)
mapk.cor <- findCorrPartners(mapk.syn, subset.loring.eset, remove.these.genes)