getPwayGenes {attract} | R Documentation

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

### 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)

[Package attract version 1.42.0 Index]