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

In GenomeGraphs: Plotting genomic information from Ensembl

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

displayProbesets:

Object of class "logical" used to indicate if probe set names should be plotted or not

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))
}

GenomeGraphs documentation built on Oct. 31, 2019, 4:34 a.m.