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
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