getCustomGenes: Function removes genes from the custom pathway that...

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

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.

Details

This function is also called internally by findSynexprs.

Value

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

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)
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)

attract documentation built on Nov. 8, 2020, 8:04 p.m.