PLINK output summaries - Githubissues

ohsu-comp-bio / cedar-gwas

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PLINK output summaries #1

Open adamstruck opened 6 years ago

adamstruck commented 6 years ago

Create an Rscript that does the following given a directory of PLINK output files:

[ ] identify PLINK output type
[ ] report min p value
[ ] report summary statistics (quartiles, etc.)
[ ] report test metadata (project, phenotype, test type, etc.)
[ ] if min p value <= some threshold keep output file otherwise delete it
[ ] generate plot if min p value <= some threshold

adamstruck commented 6 years ago

~PLINK docs: http://zzz.bwh.harvard.edu/plink/index.shtml~

We are using 1.9b4 so the docs are here: https://www.cog-genomics.org/plink/1.9/formats