Could someone help me please.
I have a gene of interest. In that gene, I have: SNP information for two loci (SNPa and SNPb) in that gene for 10 people, and the age of diagnosis of a disease of the individual.
What I want is to have a table with four columns: a person ID, age of disease diagnosis, do they have SNPa, do they have SNPb for this gene.
(after this step, I want to look at whether the people with SNPa tend to live longer with the disease than those with SNPb, using the Cox model).
I'm new to PLINK.
I know that the .bed file is a binary file with the genotypes of my individuals. I know the names of the SNPs (ss names) that I want to know whether the individuals have or not.
Would someone know the command for PLINK that says "go to the relevent file (probably the .bed file), return a list of individuals with SNPa (i.e. individual's ID, and that they have a SNP at this point). Then I can run the same command for SNPb, and then make the table described above based on whether the SNP is present.