R1 clustering in MONET dosent work

[Jordi-Valls]

Hi collegues,

sorry to open this issue, but I'm not able to execute R1 clustering mode. I tried to follow other issues that talk about "'problem too large' and I cannot understand how to solve it.... This is my output error:

R1: Running Team Causality's code from the DREAM challenge on disease module identification [1] "/R1_code/sub-challenge1"

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

decompose, spectrum

The following object is masked from 'package:base':

union

Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105 Calls: main ... generateFile -> as.matrix -> as.matrix.Matrix -> as -> asMethod Execution halted

Which is similar than other issues. I execute monet by default with my network file, and the error persist.... I will appreciate a detailed steps to execute R1 correctly.

Thanks for your time

Jordi

[mattiat]

Dear Jordi, this issues reminds me of https://github.com/BergmannLab/MONET/issues/15 We actually have open branches where we were trying to solve this: https://github.com/BergmannLab/MONET/tree/issues_15 and https://github.com/BergmannLab/MONET/tree/issues_15_2 @WeijiaZhang24: what is the status? Can you finish this up?

[mattiat]

Dear Jordi, some updates: Weijia says: "I had a look on the problem again and believe that the cause is how the code of R1 method handles node ID inputs. The R script calls a C executive which constructs matrix from the input. If the input has large node ID, e.g., Node 99999, then matrix of 99999*99999 size will be constructed, even if the input actually only has a few nodes. If this is indeed the case, I should be able to fix it next week". We all started new jobs and are quite busy, thank you for your patience!

Cheers, Mattia

[WeijiaZhang24]

@mattiat I created a pull request for the fix. @Jordi-Valls would you please confirm (after Mattia has merged the pull request) whether this solves your problem?

[mattiat]

Merged, thank you @WeijiaZhang24 for pushing a fix and testing it. @Jordi-Valls Please let us know if things work for you.

[Jordi-Valls]

Okay @mattiat and @WeijiaZhang24 , thanks for your help, I will reinstalled MONET and I will tell you if I can run R1 properly.

Best,

Jordi