getEsPositions {phenoTest} | R Documentation |
Given an object of class epheno obtain the gene positions on the genome.
getEsPositions(epheno, phenoName, organism = "human", logEs = T, center = FALSE)
epheno |
An object of class |
phenoName |
The phenotype that we want to use. Has to be in |
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. |
The output will usually be passed to findCopyNumber.
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.
Evarist Planet
data(epheno) phenoNames(epheno) mypos <- getEsPositions(epheno,'Relapse') head(mypos)