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  • CummeRbund: populate db

    I am a complete nube when it comes to CummeRbund and SQL, so I apologize for this very simple question. I read the following in the CummeRbund manual:


    populate the 'cu ffData.db' database backend, and return the Cu ffSet pointer object, you can do the following.

    > library(cummeRbund)
    > cuff<-readCufflinks()
    > cuff

    CuffSet instance with:
    3 samples
    400 genes
    1203 isoforms
    662 TSS
    906 CDS
    1062 promoters
    1986 splicing
    990 relCDS


    sorry, I am embarrassed asking this question but what exactly is going on in the above example. If I do this, does this mean my db is "populated"?

  • #2
    This basically means cummeRbund will read in the cuffdiff output files and write the information in a database, that remains in your working directory and can be reloaded fast. Then cummeRbund works on that database.

    Comment


    • #3
      sorry, it was not the most intelligent question.

      Thank you very much sBeier

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