getGenes {pathVar} | R Documentation

## Gets significant genes within a certain window of variability.

### Description

Gets significant genes within a certain window of variability.

### Usage

    getGenes(pvalue_results,pathway,window)

### Arguments

`pvalue_results` | output of `pathVarTwoSamplesCont` step.
`pathway` | A pathway name.
`window` | A `vector` with a min and max range to specify the window of genes to grab with a certain level of variance.

### Details

It takes the result of `pathVarTwoSamplesCont`, a given pathway and "window". It will give you the genes having their variability value in the window for group 1 and another set of genes for group 2 corresponding to the given pathway. It also returns the set of all the genes from your dataset that belong to this pathway.

### Value

An object of class `geneSet` with 3 properties. The first 2 are the genes in the window from each group. The third are all the genes.

### Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

### Examples

    # we run the 2 samples analysis on the first 10 pathways from kegg
    pways.kegg.10pways <- lapply(pways.kegg, function(x) x[1:10])
    results_2samples=pathVarTwoSamplesCont(bock,pways.kegg.10pways,groups=as.factor(c(rep(1,10),rep(2,10))))
    genes_window=getGenes(results_2samples,pways.kegg$PATHNAME[10],c(0.25,075))

[Package pathVar version 1.20.0 Index]