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
?