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rivas-lab / hla-assoc

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Create file with plink results, add to repo #2

Open cdeboever3 opened 5 years ago

cdeboever3 commented 5 years ago

Combine the .hybrid files in /oak/stanford/groups/mrivas/users/jolivier/repos/hla-assoc/data/PLINK_results into one file. We only need rows where the TEST column has value ADD and we only need the following columns:

ID     FIRTH?  TEST    OBS_CT  OR      SE      T_STAT  P

You'll need to a column with the phenotype code. Make the file a tsv and gzip it before adding to repo.

cdeboever3 commented 5 years ago

I started doing this in the Process Plink Results notebook. I think Julia was processing these plink files a bit in her compare_cutoff_pvals notebook as well. I'm trying to reconcile the number of diseases and alleles left after filtering based on disease/allele frequency right now before making a filtered version of the file.

guhanrv commented 5 years ago

I think the folder /oak/stanford/groups/mrivas/users/jolivier/repos/hla-assoc/scripts/output/process_output/ should have files of the form _processed.txt, which should have the odds ratio, p value, and log odds ratio from both R and PLINK (PLINK would be the first columns, not labeled with (R)) On Feb 3, 2019, 7:54 AM +0530, Christopher DeBoever notifications@github.com, wrote:

I started doing this in the Process Plink Results notebook. I think Julia was processing these plink files a bit in her compare_cutoff_pvals notebook as well. I'm trying to reconcile the number of diseases and alleles left after filtering based on disease/allele frequency right now before making a filtered version of the file. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or mute the thread.