getEsPositions {phenoTest} | R Documentation

## Obtain chromosome positions for each gene.

### Description

Given an object of class epheno obtain the gene positions on the genome.

### Usage

    getEsPositions(epheno, phenoName, organism = "human", logEs = T, center = FALSE)

### Arguments

`epheno` | An object of class `epheno` usually obtained with `ExpressionPhenoTest`
`phenoName` | The phenotype that we want to use. Has to be in `phenoNames(epheno)`
`organism` | Has to be 'human' or 'mouse'. The default is 'human'.
`logEs` | If the values have to be log scaled.
`center` | If the values have to be genome centered. If TRUE the genome average will be substracted to every value.

### Details

The output will usually be passed to findCopyNumber.

### Value

An object of class `data.frame` will be returned containing 3 variables: es (enichment score for fold change or hazard ratio), chr (chromosome), pos (position in Mb). epheno's featureNames will be used as row names.

### Author(s)

Evarist Planet

### Examples

    data(epheno)
    phenoNames(epheno)
    mypos <- getEsPositions(epheno,'Relapse')
    head(mypos)

[Package phenoTest version 1.38.0 Index]