findCorrPartners {attract} | R Documentation |
This function finds genes with expression profiles highly correlated to a synexpression group.
findCorrPartners(mySynExpressionSet, myEset, removeGenes = NULL, cor.cutoff = 0.85, ...)
mySynExpressionSet |
|
myEset |
|
removeGenes |
|
cor.cutoff |
numeric value specifying the correlation cut-off. |
... |
additional arguments. |
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
.
A SynExpressionSet
object which stores the genes that are highly correlated with the synexpression group provided, and their average expression profile.
Jessica Mar
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)