ExonArray-class: Class "ExonArray" representing probe level exon array data from Affymetrix

Description

Represents probe level exon array data from Affymetrix. Makes it possible to visualize alternative splicing as measured by the Affymetrix exon array platform and relate it to known transcript isoforms annotated by Ensembl

Arguments

Objects from the Class

Objects can be created by calls of the form new("ExonArray", ...).

Extends

Class "gdObject", directly.

References

http://www.stat.berkeley.edu/~steffen/

Examples

Run this code

if(interactive()){
data("unrData", package="GenomeGraphs")
library(biomaRt)
mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

title = new("Title", title ="ENSG00000009307", dp = DisplayPars(color = "darkslategray"))
exmapcol = rep("khaki", length(unrNProbes))
exmapcol[28]="darkred"
probeSetCol = rep("grey", length(unrNProbes))
probeSetCol[27:28]="darkslategray"
probeSetLwd = rep(1, length(unrNProbes))
probeSetLwd[27:28]=3

exon = new("ExonArray", intensity = unrData, probeStart = unrPositions[,3], probeEnd=unrPositions[,4], probeId = as.character(unrPositions[,1]), nProbes = unrNProbes, dp = DisplayPars(color = "blue", mapColor = exmapcol, probeSetColor = probeSetCol, probeSetLwd = probeSetLwd), displayProbesets=FALSE)
exon2 = new("ExonArray", intensity = unrData, probeStart = unrPositions[,3], probeEnd=unrPositions[,4], probeId = as.character(unrPositions[,1]), nProbes = unrNProbes, dp = DisplayPars(color = "blue", mapColor = exmapcol, probeSetColor = probeSetCol, probeSetLwd = probeSetLwd, plotMap=FALSE), displayProbesets=TRUE)

affyModel = new("GeneModel", exonStart = unrPositions[,3], exonEnd =  unrPositions[,4])
gene = new("Gene", id = "ENSG00000009307", biomart = mart)
transcript = new("Transcript", id ="ENSG00000009307" , biomart = mart)
legend = new("Legend", legend = c("affyModel","gene"), dp = DisplayPars(color= c("darkgreen","orange")))

gdPlot(list(title,exonarray1 = exon2,exonarray2= exon, AffymetrixModel= affyModel, gene, transcript, legend), minBase = min(exon@probeStart), maxBase=max(exon@probeEnd))
}