Merging Outputs from plink --assoc and --hardy to Produce Table
Good day, I have summary statistics of my APOBEC3 gene which were generated using plink --assoc. I have also used plink --hardy to assess deviation from hwe. Now I need to translate these summary stats into a publication ready table that shows frequency and distribution of the apobec3g genotypes and their association with HIV status. is there an R or even pandas script that I can use to do this? I am new to R scripting and have limited python scripting skills
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As long as the output of assoc is 1 row per SNP, then rows should match with hardy output, we can use
paste:Thank you so much. How about calculating allelic odds ratios? Which plink/R command can I use for that?