shirley zhang | 9 Apr 03:03 2013
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Replace the ensemble annotation with UCSC knownGene track in library "GenomeGraphs"

Dear List,

I have been successfully using library "GenomeGraphs" to draw a figure with
affy's exon array intensity data and Ensemble 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 <at> 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))

> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GenomeGraphs_1.8.0 biomaRt_2.4.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-3 XML_3.1-1

Many thanks,
Shirley

<zhangxl@...>

<zhangxl@...>

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