phenoTest (version 1.20.0)

getEsPositions: 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.

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.

Details

The output will usually be passed to findCopyNumber.

Examples

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