getPwayGenes {attract} | R Documentation |
Function removes genes from the chosen pathway that demonstrate little variation across the cell types.
getPwayGenes(pathwayIds, myAttractorModuleSet, removeGenes = NULL)
pathwayIds |
a single character string denoting the KEGG or reactome ID of the pathway module to be analyzed. |
myAttractorModuleSet |
|
removeGenes |
|
This function is also called internally by findSynexprs
.
A vector
of gene names that have variable expression across the different cell types in a pathway.
Jessica Mar
Mar, J., C. Wells, and J. Quackenbush, Defining an Informativeness Metric for Clustering Gene Expression Data. to appear, 2010.
## 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) map.syn <- getPwayGenes("04010", attractor.states, removeGenes=remove.these.genes) ## End(Not run)