genesInArea: Find genes that are in given areas.

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

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)

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