Question: How To Replace The Ensembl Annotation With Ucsc Knowngene Track In Library "Genomegraphs" (Bioconductor)
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gravatar for shirley0818
6.3 years ago by
shirley081890
United States
shirley081890 wrote:

Dear All,

I have been successfully using library "GenomeGraphs" to draw a figure with affy's exon array intensity data and Ensembl geneAnnotaion track. My qustion is how can I replace the Ensembl transcript annotation track with UCSC knownGene track or NCBI's RefSeq track? Below is my code for Ensembl track

library(GenomeGraphs)
mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")

title <- makeTitle(text = "Test")
exon <- makeExonArray(intensity = arrayData)
affyModel.model <- makeGeneModel(start = unrPositions$start, end = unrPositions$stop)
affyModel <- makeAnnotationTrack(start = unrPositions$start, end = unrPositions$stop, feature = "gene_model",group = geneid[i], dp = DisplayPars(gene_model = "darkblue"))

transcript<-new("Transcript",id=unique(gene@ens[,"ensembl_gene_id"]),biomart=mart,dp=DisplayPars(plotId=TRUE))

plusStrand <- makeGeneRegion(chromosome = as.character(unrPositions[1,"seqname"]),start = min(unrPositions$start), end = max(unrPositions$stop), strand = as.character(unrPositions[1,"strand"]), biomart = mart)
gdPlot(list(title, exon,  affyModel, ga, transcript, legend), minBase = min(unrPositions$start),maxBase = max(unrPositions$stop))

Shirley

R bioconductor ucsc • 1.8k views
ADD COMMENTlink modified 6.3 years ago by Istvan Albert ♦♦ 80k • written 6.3 years ago by shirley081890
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