How to change group names with cummeRbund

Question

[mandar.bobade]

Hi everyone,

I am using cummeRbund for cuffdiff data presentation. I have time series data, with three multiple groups, i.e. treatment-1, treatment-2 and treatment-3. While generating cuffdiff results, I had forgotten to keep these group names uniform, say T1, T2 and T3 insteat I kept T1, T-2 and T-3. My question is, how could I change these group names with cummeRbund while generating graphs, such as box plot, dendrogram, histogram, volcano plot, etc. It would be of great help if someone guides me in this aspect.

Regards,

Mandar

Answer 1

[mandar.bobade]

I found way out, not completely but served the purpose.

U will have to first delete .db file, if not deleted it won't overwrite .db I guess and throws error, which was previously been created while running cummeRbund. Then use linux command "sed -i 's/T1/T-1/g' *.*" from inside the cuffdiff output directory. And, then rerun your R-script for graphs. Since changing the legends everytime with each type of graphs in cummeRbund is cumbersome job, this will save u from running cuffdiff again. Simple but had made me scared a lot..