Understand glm interaction command in plink2
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15 months ago
jfertaj ▴ 100

Hi,

I have a very naive question but I don't quite understand the --parameters option for --glm in plink and the output of the logistic regresion.

I have a binary phenotype with 3 covariates HAP, BMI, and SEX

I have run plink2 with --glm interaction command and --parameters 1-4, 6 (1st run), and --parameters 1-6 (2nd round).

For the same SNP, obviously I get two outputs

1st run

22  25601465    rs113538872 C   T   ADD 958 0.0918304   2.2693  -1.05222    0.292698
22  25601465    rs113538872 C   T   SEX  958    0.768992    0.155539    -1.68881    0.0912562
22  25601465    rs113538872 C   T   HAP     958 1.32753 0.244267    1.15988 0.246096
22  25601465    rs113538872 C   T   BMI 958 0.989258    0.00873278  -1.23677    0.216172
22  25601465    rs113538872 C   T   ADDxSEX 958 2.242   0.67785 1.19107 0.233625
22  25601465    rs113538872 C   T   ADDxHAP 958 0.847376    1.019   -0.162522   0.870895

2nd run
22  25601465    rs113538872 C   T   ADD 958 0.372173    1.91994 -0.514807   0.606688
22  25601465    rs113538872 C   T   SEX  958    0.802544    0.151079    -1.45598    0.145398
22  25601465    rs113538872 C   T   HAP     958 1.32871 0.244131    1.16417 0.244356
22  25601465    rs113538872 C   T   BMI 958 0.989452    0.00872802  -1.2149 0.224403
22  25601465    rs113538872 C   T   ADDxHAP 958 0.765515    1.00908 -0.264802   0.791162

My question is:

can I interpret that the row with ADD in first run is the result of running the model TRAIT ~ SNP + SEX + HAP + BMI + SNP:SEX + SNP:HAP, and the row with ADD in the second run is the result of running this model TRAIT ~ SNP + SEX + HAP + BMI + SNP:HAP?

If I am correct, which model corresponds to ADDxHAP? or ADDxSEX?

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