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ewouddt / CCCBiclust

R Wrapper for (e-)CCC Biclustering Algorithm
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how is the discretization step defined in the CCC and eCCC? #1

Open HVoltBb opened 5 years ago

HVoltBb commented 5 years ago

Both CCC and eCCC are manipulating a discretized expression matrix. So, how is the discretization defined here? Is there a way to customize its settings in R?

I have used BIGGeST before, and it is customizable there.

Thanks,

ewouddt commented 5 years ago

Hi HVoltBb,

This package is a R wrapper for the already existing Java software from the original authors to apply the CCC and eCCC algorithms. You could check the original documentation of their java application, but I think the discretization is baked into the java code. See the top of page 6 for the discretization procedure that is used by the original authors in their paper: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.99.8878&rep=rep1&type=pdf

If you really want to apply your own discretization procedure I suppose you could:

  1. Discretize your own dataset to "Downregulated"(=D), "Upregulated" (=U) and "No Change"(=N).
  2. Use your discretized data matrix (with D, U and N) to "simulate" a dataset which their discretization procedure would discretize to the same D, U, N data matrix. (Probably taking outrageous changes from 1 to 1000 for upregulated, 1000 to 1 for downregulated and 1 to 1 for no change, would work).

Hope this helps!

HVoltBb commented 5 years ago

Thanks a lot for your timely reply. I tried to find their software documentation but found that their website is offline now. I'll read that paper you provided.

It seems they are only using an alphabet with three elements. I was thinking about cases with more than 3 elements. According to the paper you sent me, they just implemented the three element case, right? If it is the case, you can close this issue.

HVoltBb commented 5 years ago

Hi, One more question. Do you happen to have the source code of the Java program?

There website is offline and they, the original authors of those Java programs, are not responding to my emails.

Thanks

ewouddt commented 4 years ago

Hey, sorry for the late answer! I'm afraid I only have the jar files of the program which you can find in the inst/java/ folder.