Question: How to get UCSC url when use rtracklayer, contain the track in the url ,it may be very useful
gravatar for zhangqshxxzz
11 months ago by
zhangqshxxzz0 wrote:

Dr Michael Lawrence:

Hellp, I use the rtracklayer to product the UCSC show with track, it work very well. But if the aim region are too much, is there have a option can direct get the UCSC url with the track, not the opened HTML........

It will very convenience to annotation the region file in bath, when use for cnv discover and annotation.





ADD COMMENTlink modified 11 months ago by James W. MacDonald48k • written 11 months ago by zhangqshxxzz0

session <- browserSession()
genome(session) <- "hg19"
export(region, "Track12.bed")
restoredTrack2 <- import("Track12.bed")
track(session, "Track") =  restoredTrack2
browserView(session,restoredTrack2*-10,hide=c("UCSC Genes","GTEx Gene","ENCODE Regulation...",
                                              "Conservation","Common SNPs(150)","RepeatMasker"),
            pack=c("Track","DECIPHER","RefSeq Genes","ClinGen CNVs","ClinVar Variants",
                   "GeneReviews","OMIM Genes","DGV Struct Var")  )

and also when I RUN the command ,it is work well before , now it report the error like this....

Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : 
  'names' attribute [211] must be the same length as the vector [209]
In addition: Warning message:
In readChar(f, 1) : can only read in bytes in a non-UTF-8 MBCS locale

ADD REPLYlink written 11 months ago by zhangqshxxzz0

Should be fixed as of rtracklayer 1.38.2.

ADD REPLYlink written 11 months ago by Michael Lawrence10k
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