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  • Q:Accessing Functional data with CummeRbund from Cufflinks

    Hello,

    I am fairly new to the cummeRbund R-package and R.
    For my research I would like to focus on functional properties between my conditions. Even though cufflinks output has created a file called gene_exp_func.diff, I couldn't think of a way to a access the data through cummeRbund. EXCEL shows me that the gene_exp_func.diff has columns for KOG_class, pathway, etc..
    Is there a way to access the functional groups (KOG, pathway) and sort for KOG_group "CELLULAR PROCESSES AND SIGNALING" for example? Then I would also like to count the hit for the KOG_groups and create simple piecharts. Any suggestions, please?

    Furthermore, I was wondering if there is a recommendation or accepted procedure for averaging expression levels in such groups as above, such as all hits in a KOG_group. Is a simple average of the log2fold values acceptable or should the expression values 1 and 2 be used and log2fold be calculated?

    Thanks for your valuable suggestions.

    Saint-Louis

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