Question: How To Caculate The Or Value Of Additive Model With Plink
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gravatar for bluegenechip
7.0 years ago by
bluegenechip0 wrote:

I am learning the plink software now. I wondering what command can caculate the OR value of additive model with plink. Is it the ADD value in the result of the "plink --logistic" command?or the ADD value in the result of the "plink --logistic--genotypic" command?or other else? Thank you very much.

At the plink homepage: The TEST column is by default ADD meaning the additive effects of allele dosage. Adding the option --genotypic will generate file which will have two extra tests per SNP, corresponding to two extra rows: DOMDEV and GENO_2DF which represent a separate test of the dominance component or a 2 df joint test of both additive and dominance (i.e. corresponding the the general, genotypic model in the --model command).

I can understand this sentence "The TEST column is by default ADD meaning the additive effects of allele dosage." is response to the forward command-"plink --bfile mydaya --logistic", or response to the backward command-"plink --bfile mydaya --logistic --genotypic".

model plink • 3.1k views
ADD COMMENTlink modified 5.3 years ago by chrchang5235.0k • written 7.0 years ago by bluegenechip0
1

Note that plink2 is released and it is a lot faster... https://www.cog-genomics.org/plink2/

ADD REPLYlink written 5.3 years ago by Floris Brenk890
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gravatar for chrchang523
5.3 years ago by
chrchang5235.0k
United States
chrchang5235.0k wrote:

The seventh column of the --logistic report should be titled 'OR', and contain the odds ratios you want.

ADD COMMENTlink written 5.3 years ago by chrchang5235.0k
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