ExonArray-class {GenomeGraphs} | R Documentation |
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 can be created by calls of the form new("ExonArray", ...)
.
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
Class "gdObject"
, directly.
signature(object = "ExonArray")
: ...
Steffen Durinck
http://www.stat.berkeley.edu/~steffen/
objects to See Also as gdPlot
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)) }