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saezlab / CARNIVAL

CAusal Reasoning for Network Identification with integer VALue programming in R
https://saezlab.github.io/CARNIVAL/
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generate_measfile() returns: object 'folderpath' not found #18

Closed dereckmezquita closed 4 years ago

dereckmezquita commented 4 years ago

Tried to rerun some code written just a couple of weeks ago. Getting this error now when generating the measurement file.

I noticed that the folderpath variable is declared inside the generate_measfile() function but not defined.

Moreover, I cannot find the generate_measfile() in the source code you currently have available. Have you changed the name or otherwise?

I pasted my error below:

> generate_measfile(measurements = TF_uniprot, \+ topnumber = NULL, \+ write2folder = "measurements") Error in paste0(folderpath, "/meas_", drug, "_all.txt") : object 'folderpath' not found

enio23 commented 4 years ago

Hello,

Yes indeed, generate_meas() function and few others have been removed since I had to adapt the CARNIVAL pipeline according to Bioconductor guidelines and requirements. In case you are integrating TF and pathway activity scores, I will soon add an example in the README about how one can do that. But for this I am waiting for the new release of Bioconductor packages where CARNIVAL and newest versions of PROGENy and DoRothEA packages will be there. This is expected to happen in the next few days within this mont but if you need any urgent help you can contact me at enio.gjerga@gmail.com.

Best,