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
:"matrix"
, array data
matrix containing probes as the rows and samples as the columnsprobeStart
:"numeric"
vector with the start positions of the probesprobeEnd
:"numeric"
vector with the end positions of the probesprobeId
:"character"
vector containing the probeset identifiersnProbes
:"numeric"
vector defining how many probes there are for each exon/probesetsize
:"numeric"
specifying the size of the ExonArray plot in the final plotdisplayProbesets
:"logical"
used to indicate if probe set names should be plotted or notprobesetSize
:"numeric"
font size of the probeset identifiers to be plotted color
:"character"
vector of
colors or one color that will be used to draw the intensity values mapColor
:"character"
specifying the color of the lines that map the probeset positions to the Ensembl gene annotationlwd
:"numeric"
vector of line widths to be used to plot the intensity data.lty
:"character"
vector of line types to be used to plot the intensity data.
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)) }