cbiagii / cetf Goto Github PK

Dear, I am trying to analyze scRNA data but I have some issues. Could you please tell me how to input the data?
Thanks

Dear maintainers,
I was very enthusiastic about cetf package and want to thank you for this useful package.
I have two questions about this package:
Question 1 : I was wondering if the RIF scores providing in the RIF analysis are RIF Zscores ? Or do we have to transform the RIF score in Zscores by ourself?
Question 2 : I was wondering if it is possible to use it with paired samples ie I have two conditions (CTRL and TRT) but I want to take into account the fact that for each animal, we have the CTRL and the TRT samples.
So I have 10 animals : (from A1 to A10) and 10 samples control and 10 samples treated.
In DESeq2 my design is as follow :
Design(dds)<-~animal + treatment.
I’m blocked in CeTF pipeline because I don’t know how to explain to CeTF such a case ...can you help me please ?
Last but not least, I would recommend in the vignette to start by RIF analysis than PCIT one. Because at first, we identified TFs in our dataset and then perform PCIT analysis.
Thanks you in advance for yours answers.

Hi CeTF authors
I'm testing your PCIT function with a correlation matrix (I give the original dataframe an it's converted to this matrix) of 1000x1000 elements and the function take several minutes to complete. I want to use this function with 10/20 times the size of this test. How I can speed up this process? The original PCIT package did parallelize the computation and the results were obtained in a reasonable time. Is this a complete new implementation?

Thank you in advance
Pedro Seoane

Has anyone else tried running PCIT on 3 samples and run into some issues with the PCIT output values? When I did, I got lots of zeros for the corr2 values and, in turn, this reduced the amount of Key TF's with freq and freq.diff values. PCIT works fine for me with 5 samples.

Thanks!

Hi CeTF authors
I used the PCIT and RIF algorithm a long time until the PCIT package was removed in R4. When I applied the RIF processing to my data, I performed first the PCIT algorithm onto the correlation matrix to keep only the significant connections. Checking your RIF function code, I cannot found any call to PCIT. Is it encapsulated in any other function or you don´t apply PCIT for RIF calculation?
Thank you in advance
Pedro Seoane