Question: Genome MuSic Mutation Relation RUntimes
1
gravatar for Ido Ben-Zvi
2.2 years ago by
Ido Ben-Zvi10
Ido Ben-Zvi10 wrote:

Hi,

I am trying to run the MuSic analyses on a some cohort data that I have. I am using a 4cpu 2xl EC2 machine. I have been able to apply all analyses up to mutation-relation (MRT). Here the application has been running for several days (running several cohorts in parallel, with sizes ranging between 20 and 200). Non of the runs have completed. Previously, even the most extensive calculations on these cohorts did not take up more than 24h.

Looking at the code I see potentially endless loops such as:

        doit=1;
        while(doit==1)
        {
            xi=matrix.sample.v1(x);
            if (max(xi)==1) doit=0;
        }

But there could also be less obvious pitfalls, as R loops - looking for restricted permutations.

Can anyone share from their experience running this? Should I abandon ship?

 

Thanks,

Ido

 

ADD COMMENTlink modified 2.2 years ago by Cyriac Kandoth4.7k • written 2.2 years ago by Ido Ben-Zvi10
1
gravatar for Cyriac Kandoth
2.2 years ago by
Cyriac Kandoth4.7k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth4.7k wrote:
Unfortunately it scales exponentially with the number of genes you're testing. I wouldn't run it on more than 30 genes. There are much better alternatives to this pairwise gene test, assuming you're trying to find pathway-level relations. Try MultiDendrix, MeMO, MUTEX, CoMet, etc.
ADD COMMENTlink written 2.2 years ago by Cyriac Kandoth4.7k

Thank you Cyriac

ADD REPLYlink written 2.2 years ago by Ido Ben-Zvi10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 623 users visited in the last hour