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
The file has a header line. Why are you ignoring it?
Every time you run plink, it prints a URL pointing to online documentation. Why are you ignoring that, too?
Thank you for pointing that out @chrchang523. I appreciate your time and effort in helping me out :). But to answer your questions, I have definitely not ignored any of the things you mentioned because they are all part of the analysis and understanding. But I find PLINK difficult to comprehend 100%, after six months of on and off with PLINK, i thought I'd try and seek help. I don't think this platform should be used to put people down. We are not trying to find an easy way out, we are trying to understand.
I stand by the harsh tone of my comment, because you did not include the header line in your question. There is simply no excuse for that when you are asking what the columns mean.
(edit: ok, I see that you have edited in the column headers. Now we can get somewhere.)