getCoordGeneSets: extract coordinates gene sets

In esetVis: Visualizations of expressionSet Bioconductor object

Description

extract coordinates gene sets

Usage

getCoordGeneSets(dataPlotGenes, geneSets, esetUsed, geneSetsVar = list())

Arguments

dataPlotGenes	data.frame with two columns 'X' and 'Y' with coordinates for the genes
geneSets	geneSets list of gene sets, e.g. gene pathways, output from the 'getGeneSets' function in MLP the genes IDs must correspond to the sampleNames in the eset
esetUsed	expressionSet (or SummarizedExperiment) object with data
geneSetsVar	variable of the featureData used to match the genes contained in geneSets, most probably ENTREZID, if NULL the featureNames of the eSet are used

Value

data.frame with two columns 'X' and 'Y' with coordinates for the gene sets

Author(s)

Laure Cougnaud

Laure Cougnaud

esetVis documentation built on Nov. 8, 2020, 4:51 p.m.