getEsPositions: Obtain chromosome positions for each gene.

In phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

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)

phenoTest documentation built on Nov. 8, 2020, 7:53 p.m.