I am trying to write the right command for my association testing using PLINK 1.9 but I could not find a clear answer so far and not sure how to wrtie it correct.
I have genotype variants called and in PLINK bed formatted files under geno_data folder.
I have phenotype.txt file. First column as "Sample_ID", second column as "Treatment" (1 for Placebo and 2 for CompoundX) and third column has the Response variable as "ResX", which has integer number between 0 to 9.
I also have PCs file as cov.txt. The first and second columns are the same and includes Sample_IDs. The column names are "FID" and "IID". The third, fouth and fifth columns have PCs,with the column names "PC1", "PC2" and "PC3".
The Plink documentation did not help me as I am new in this. Therefore I need some examples command to clarify for various models as described below.
I need the correct PLINK (1.9) command (if not possible PLINK2 is also OK) for the following linear models:
Model 1:
ResX ~ Variant * Treatment + PC1 + PC2 + PC3
Second command I need is for this model:
Model 2:
ResX ~ Variant + Treatment + PC1 + PC2 + PC3
Model 3:
ResX ~ Variant * Treatment
Note I had asked this question on Biostar 11 days ago but did not receive any answer or comment yet. Thank you
