I'm struggling with PLINK and the results being generated by PLINK. I'm not sure which one to look at and consider any statistical significance.
I'm using a SNP data from a control/case study. I firstly did the basic association analysis using the following command:
plink --file xxx --assoc --ci 0.95 --out newfile
which generated a file with p values for each SNPs including an OR and L/U95 etc.
I then wanted to use the logistic regression command, which I have a covariate file that consists of 3 columns (FID, IID, and a covariate which i will call (CN), so I wanted to see if the covariate has an effect on phenotype or the outcome:
plink --file xx --logistic --covar covariate.txt --covarname CN --ci 0.95 --out newfile
which gave me the following results:
CHR SNP BP A1 TEST NMISS OR STAT P 8 SNP1 6962046 G ADD 1058 0.646 -3.607 0.00031 8 SNP1 6962046 G CN 1058 0.9289 -1.9 0.05737
I'd really appreciate it if someone explained to me what the results mean? also, the SNP1 from the assoc analysis showed with a P-value of (2.95E-06), I don't know if that would help.
I just want know what kind of command to use to generate an output knowing the effect of my covariate to the phenotype and how to interpret it. I have also used the
--genotypic command in the logistic regression analysis but it has given me different p values and OR. which test do I need to use?
--genotypic flag with
--logistic gererated an output that looks like this:
CHR SNP BP A1 TEST NMISS OR SE L95 U95 STAT P 8 SNP1 6962046 G ADD 1058 0.6935 0.1951 0.4731 1.016 -1.876 0.06063 8 SNP1 6962046 G DOMDEV 1058 0.8997 0.2302 0.573 1.413 -0.4593 0.646 8 SNP1 6962046 G CN 1058 0.93 0.03887 0.8618 1.004 -1.868 0.06183 8 SNP1 6962046 G GENO_2DF 1058 NA NA NA NA 13.32 0.001284