Hi,
I am fairly new to the CummeRbund R package and R in general.
After a Tophat - cufflinks procedure I would like to evaluate the data with CummeRbund. I would like to investigate differences at the functional level by using KOG_classes or pathway_classes from the annotated genes.
We created gene_exp_func.diff in the cufflinks output folder, which contains (when opened in EXCEL) the information I am interested in. However, in CummeRbund I have not found a way to access the functional classification and for example create lists and graphs (pie chart) summarizing the transcripts in each KOG_class that are significantly different between my conditions.
Are there codes to access this information and create such graphs in R?
Thanks,
Saint-Louis
I am fairly new to the CummeRbund R package and R in general.
After a Tophat - cufflinks procedure I would like to evaluate the data with CummeRbund. I would like to investigate differences at the functional level by using KOG_classes or pathway_classes from the annotated genes.
We created gene_exp_func.diff in the cufflinks output folder, which contains (when opened in EXCEL) the information I am interested in. However, in CummeRbund I have not found a way to access the functional classification and for example create lists and graphs (pie chart) summarizing the transcripts in each KOG_class that are significantly different between my conditions.
Are there codes to access this information and create such graphs in R?
Thanks,
Saint-Louis