cummeRbund Accessing class_code

[Edden]

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

  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.

[Edden]

Any suggestions?

[mra]

You can use this command instead:

isoforms.features <- features(isoforms(cuff))

be sure to had supplied the merged.gtf file when calling readCufflinks().