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  • cummeRbund Accessing class_code

    First a warm Hello to erveryone,

    I've been passively reading here for a while and learnt a lot.
    Now, I also have a question:

    How can I access the class_code wit cummeRbund?


    using
    Code:
      gene.features <- features(genes(cuff))
    only gives "NA" for the class_code.

    In general, I am interested in new intergenic transcripts (class_code u) and would like to access the following features:

    -ID
    -Location (strand, chromosome, position)
    -FPKM values
    -Differential expression

    I have 12 sampels from unpaired Illumina RNAseq data. So far, I've followed the protocoll from Trapnell (nature 2012). After merging, I ran cuffcompare telling me there are ~260 genes with class code u. Now after running cuffdiff, I would love to know which ones are diff. expr.

  • #2
    Any suggestions?

    Comment


    • #3
      You can use this command instead:

      Code:
      isoforms.features <- features(isoforms(cuff))
      be sure to had supplied the merged.gtf file when calling readCufflinks().

      Comment

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