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xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
GNU General Public License v3.0
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Followup Question to Issue #28 #53

Closed samreenzafer closed 3 months ago

samreenzafer commented 3 months ago

Just to followup on this #28 if we don't have any known loci for our trait, do we set the input variable to NULL or should I provide an empty CSV file with only a header but no variants. ?

I tried with "NULL" and the script runs, but I'm still wondering if this is the correct way to run the script.

Thank You.

xihaoli commented 3 months ago

Hi @samreenzafer,

Yes, this is correct. If there is no known loci for your trait, then you can set known_loci <- NULL. In this case, the conditional analysis p-value should be outputted the same as the unconditional analysis p-value.

Best, Xihao

samreenzafer commented 3 months ago

Thank you for confirming!!