ExonArray-class {GenomeGraphs}R Documentation

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

Objects from the Class

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

Slots

intensity:
Object of class "matrix", array data matrix containing probes as the rows and samples as the columns
probeStart:
Object of class "numeric" vector with the start positions of the probes
probeEnd:
Object of class "numeric" vector with the end positions of the probes
probeId:
Object of class "character" vector containing the probeset identifiers
nProbes:
Object of class "numeric" vector defining how many probes there are for each exon/probeset
size:
Object of class "numeric" specifying the size of the ExonArray plot in the final plot
displayProbesets:
Object of class "logical" used to indicate if probe set names should be plotted or not
probesetSize:
Object of class "numeric" font size of the probeset identifiers to be plotted
color:
Object of class "character" vector of colors or one color that will be used to draw the intensity values
mapColor:
Object of class "character" specifying the color of the lines that map the probeset positions to the Ensembl gene annotation
lwd:
Object of class "numeric" vector of line widths to be used to plot the intensity data.
lty:
Object of class "character" vector of line types to be used to plot the intensity data.

Extends

Class "gdObject", directly.

Methods

show
signature(object = "ExonArray"): ...

Author(s)

Steffen Durinck

References

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

See Also

objects to See Also as gdPlot

Examples

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))
}

[Package GenomeGraphs version 1.2.3 Index]