genesInArea {phenoTest} | R Documentation

## Find genes that are in given areas.

### Description

Combine the output of getEsPositions and findCopyNumber to see which genes are in the enriched areas.

Given areas of enrichment (obtained with `findCopyNumber`) and a set of genes or probes and their positions in the genome (obtained with `getEsPositions`) the function tells which genes fall in each area.

### Usage

    genesInArea(x, regions)

### Arguments

`x` | An object of class `data.frame` with gene or probe identifiers as row names and the following columns: es (the enrichment score), chr (the chromosome where the gene or probe belong to) and pos (position in the chromosome in megabases). It can be obtained with the function `getEsPositions`.
`regions` | This is usually the output of `findCopyNumber` function.

### Author(s)

Evarist Planet

### See Also

getEsPositions, findCopyNumber

### Examples

    data(epheno)
    phenoNames(epheno)
    mypos <- getEsPositions(epheno,'Relapse')
    head(mypos)
    #regions <- findCopyNumber(mypos)
    #head(regions)
    #genes <- genesInArea(mypos,regions)
    #head(genes)

[Package phenoTest version 1.28.0 Index]