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  • a question about the use of R package-GenomicFeatures

    Hi,all
    i want to use the R biocondunctor package-GenomicFeatures.and i follow the manual to install this package.

    To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("GenomicFeatures")

    it sounds no problem.

    however, when i type R and enter the R command,
    >library(GenomicFeatures)
    >txdb<- makeTranscriptDbFromUCSC(genome='hg19',tablename='ensGene'),

    Error: could not find function "makeTranscriptDbFromUCSC"

    why?

    could someone help me to solve this?

  • #2
    that's weird
    i'll assume the trailing comma and space before ' ensGene' are just typos

    what does it say when you type:
    > ls("package:GenomicFeatures")
    --
    Jeremy Leipzig
    Bioinformatics Programmer
    --
    My blog
    Twitter

    Comment


    • #3
      > ls("package:GenomicFeatures")
      [1] "exons" "extractTranscriptsFromGenome"
      [3] "introns" "transcripts"

      this is the output.

      Comment


      • #4
        also, the problem happen after i deleted the space before ' ensGene'.


        Originally posted by Zigster View Post
        that's weird
        i'll assume the trailing comma and space before ' ensGene' are just typos

        what does it say when you type:
        > ls("package:GenomicFeatures")

        Comment


        • #5
          that comes from an old version of Bioconductor

          Install R 2.12.0 then reinstall Bioconductor
          --
          Jeremy Leipzig
          Bioinformatics Programmer
          --
          My blog
          Twitter

          Comment


          • #6
            all right. i will have a try.


            Originally posted by Zigster View Post
            that comes from an old version of Bioconductor

            Install R 2.12.0 then reinstall Bioconductor

            Comment

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