attract (version 1.24.0)

getCustomGenes: Function removes genes from the custom pathway that demonstrate little variation across the cell types.

Description

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

Usage

getCustomGenes(vec.geneid, removeGenes = NULL)

Arguments

vec.geneid

a vector of character strings denoting a custom gene set.

removeGenes

vector of gene names that specify those genes who demonstrate little variability across the different cellt ypes and thus should be removed from downstream analysis.

Value

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

Details

This function is also called internally by findSynexprs.

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)
# remove.these.genes <- removeFlatGenes(subset.loring.eset, "celltype", contrasts=NULL, limma.cutoff=0.05)
# vec.geneid <- c("GI_17999531-S","GI_17978503-A")
# customGenes <- getCustomGenes(vec.geneid, removeGenes=NULL)
# ## End(Not run)