Running analyses hundreds of times

[Hasuni]

Hi there, 

I am working on a project that will require running plink2 association several times (>100). This really comes down to some engineering decisions/hacks. I'm curious to see if plink2 has already existing built-in features that might make this easier. 

Some questions:

1. I see that there is a --rerun flag. Does this mean if I provide the same file to multiple runs that all the logs will be concatenated to this file?

2. Is there a way to load in a pfile once and run 10 separate analyses on it instead of reloading the pfile everytime I run the analysis?

3. Are there other features in plink2 that I should consider given the information I have shared (sorry for being vague in project scope)

[Hasuni]

Sorry, i misunderstood --rerun. This flag will just rerun an analysis using the flags from a provided log file. 

So maybe an updated question is: is there a way to avoid generating log files for every run? Is there a way to output to the same log file for all runs? 

[Chris Chang]

Some general tips:

- plink2 loads the psam and pvar files near the beginning of typical invocations.  However, it may not need to load more than the pgen's header; see the documentation on --read-freq/--error-on-freq-calc for a way to avoid the sometimes-expensive "Calculating allele frequencies..." step.
- From the --glm documentation:
"If you have multiple quantitative phenotypes with either no missing values, or missing values for the same samples, analyze them all in a single --glm run! PLINK 2.0's linear regression 'only' tends to be a few hundred times as fast as PLINK 1.9 when you analyze one quantitative phenotype at a time. But --glm also has a quantitative-phenotype-group optimization that can multiply the speedup by another factor of ~10."
- It doesn't come up much, but there is a --loop-cats flag for rerunning the same analysis on a bunch of disjoint categories.

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[Hasan Alkhairo]

Thanks Chris!! 

Also, Im running a glm using a pheno file with hundreds of phenotypes, and running this analysis several times for different groups. I created one giant pheno file that I could pass for all runs but I'm discovering some groups only have controls for some phenotypes which makes plink2 crash leaving several phenotypes unanalyzed. 

I want to avoid making several phenotype files that are specific to each groups (I have >20 groups), so is there a way to ignore these errors?

[Chris Chang]

Try —glm’s ‘skip-invalid-pheno’ modifier (

https://www.cog-genomics.org/plink/2.0/assoc#skip_invalid_pheno ).

[Hasan Alkhairo]

Worked great! Thank you so much