getCoordGeneSets: extract coordinates gene sets

Description Usage Arguments Value Author(s)

View source: R/plotTopElements.R

Description

extract coordinates gene sets

Usage

1
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. 1, 2018, 4:30 a.m.