getPwayGenes: Function removes genes from the chosen pathway that...

In jmarlab/attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Description

Function removes genes from the chosen pathway that demonstrate little variation across the cell types.

Usage

getPwayGenes(pathwayIds, myAttractorModuleSet, removeGenes = NULL)

Arguments

pathwayIds	a single character string denoting the KEGG or reactome ID of the pathway module to be analyzed.
myAttractorModuleSet	AttractorModuleSet object, output of the findAttractors step.
removeGenes	vector of probes or gene IDs (RNAseq) that specify those genes who demonstrate little variability across the different celltypes and thus should be removed from downstream analysis.

Details

This function is also called internally by findSynexprs.

Value

A vector of gene names that have variable expression across the different cell types in a pathway.

Author(s)

Jessica Mar

References

Mar, J., C. Wells, and J. Quackenbush, Defining an Informativeness Metric for Clustering Gene Expression Data. to appear, 2010.

Examples

## 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)

jmarlab/attract documentation built on May 23, 2019, 9:02 p.m.