Nothing
setMethodS3("getDetails", "ProbeLevelModel",
function(plm,probesets,id="7952953",mart=NULL,verticalBars=FALSE,geneSymbolId="external_gene_id",
transcriptClusterId="Transcript.Cluster.ID",colours="blue",lwd=1,o=NULL, verbose=FALSE) {
library("GenomeGraphs")
library("biomaRt")
cs <- getDataSet(plm)
rs <- getResidualSet(plm)
cdf <- getCdf(cs)
if (is.integer(id)) {
unit <- id
id <- getUnitNames(cdf)[unit]
} else {
unit <- which( getUnitNames(cdf)== id)
}
ind <- unlist(getCellIndices(getCdf(cs),units=unit),use.names=FALSE)
d <- log2(extractMatrix(cs,cells=ind,verbose=verbose))
r <- log2(extractMatrix(rs,cells=ind,verbose=verbose))
if(is.null(o))
o <- seq_len(ncol(d))
if(length(colours)==1)
colours <- rep(colours,ncol(d))
if(length(lwd)==1)
lwd <- rep(lwd,ncol(d))
lwd <- lwd[o]
colours <- colours[o]
d <- d[,o]
r <- r[,o]
m <- which(probesets[[transcriptClusterId]]==id) # assume this matches with the order in the CDF!!!
pm <- probesets[m,]
if( any( colnames(pm) %in% "probe_count" ))
nProbe <- pm[,"probe_count"]
else
nProbe <- rep(1,length(m))
ea1<-new("ExonArray", intensity = d, probeStart = as.numeric(pm[,"start"]), probeEnd=as.numeric(pm[,"stop"]),
probeId = rep("",length(m)), nProbes = nProbe, dp = DisplayPars(color = colours, lwd=lwd,
mapColor = "dodgerblue2",plotMap=FALSE, probeSetLwd=as.numeric(verticalBars)), displayProbesets = TRUE)
ea2<-new("ExonArray", intensity = r, probeStart = as.numeric(pm[,"start"]), probeEnd=as.numeric(pm[,"stop"]),
probeId = rep("",length(m)), nProbes = nProbe, dp = DisplayPars(color = colours, lwd=lwd,
mapColor = "dodgerblue2", probeSetLwd=as.numeric(verticalBars)), displayProbesets = FALSE)
ga <- new("GenomeAxis", add53 = TRUE)
if (verbose)
print(pm[1,])
ch <- gsub("chr","",pm[1,"seqname"])
gr<-new("GeneRegion", chromosome = ch,
start = as.numeric(min(pm[1,"start"])), end = as.numeric(pm[1,"stop"]), strand = as.character(pm[1,"strand"]), biomart = mart)
gid <- names(sort(table(gr@ens[,"ensembl_gene_id"]),decreasing=TRUE)[1])
if (verbose)
print(gid)
if( nrow(gr@ens)==0 )
gr <- NULL
if (verbose)
print(gr)
if(is.null(gid))
b <- ""
else
b <- getBM(geneSymbolId, filters = "ensembl_gene_id", values = gid, mart = mart)
ti <- new("Title", title = paste(getUnitNames(cdf)[unit],gid,b[1],sep=" -- "), dp = DisplayPars(color = "darkred"))
if( !is.null(gid) )
tr <- new("Transcript",id=gid,biomart=mart,dp=DisplayPars(plotId=TRUE))
else
tr <- NULL
returnList <- list(ti,ea1,ga,ea2,gr,tr)
keep <- !sapply(returnList,is.null)
return(returnList[keep])
}) # getDetails
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