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

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"))


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))


R bioconductor ucsc • 1.7k views
ADD COMMENTlink modified 5.8 years ago by Istvan Albert ♦♦ 79k • written 5.8 years ago by shirley081890
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1584 users visited in the last hour