buildCorMatrix {attract} | R Documentation |
Internal function - builds the correlation matrix between an average transcriptional module expression profile and a set of other genes.
buildCorMatrix(dat.fr, module.genes, cor.cutoff)
dat.fr |
a |
module.genes |
character vector specifying genes that belong in this pathway module. |
cor.cutoff |
numeric value specifying the correlation cut-off. |
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.
A character vector of genes that meet the correlation cut-off.
Jessica Mar
## 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)