Description Usage Arguments Details Value Author(s) Examples
View source: R/findAttractorsStep.R
Internal function - builds the correlation matrix between an average transcriptional module expression profile and a set of other genes.
1 | 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
1 2 3 4 5 6 7 8 | ## 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)
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