Merging Outputs from plink --assoc and --hardy to Produce Table

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6 months ago

Koketso • 0

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

PLINK PANDAS R • 484 views

ADD COMMENT • link 6 months ago by Koketso • 0

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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:

How to paste columns from separate files using bash?

ADD REPLY • link 6 months ago by zx8754 12k

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Thank you so much. How about calculating allelic odds ratios? Which plink/R command can I use for that?

ADD REPLY • link 6 months ago by Koketso • 0

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