I want to do GWAS with PLINK. I already have a data containing all the samples and have done association analyze with plink command below.
plink --bfile All_SNP.binary --make-pheno phenotype.pheno "phenoA" --aec --assoc --reference-allele All_alt_alleles --allow-no-sex --adjust --noweb --out output &
However, there are four groups of samples and I want to analyze the GWAS in two of these groups which are different phenotypes.
Is there any way indicating plink which of the two to analyze ?
The sample's information looks like this:
sample1 phenoB location1 sample2 phenoB location1 sample3 phenoA location1 sample4 phenoA location1 sample5 phenoB location2 sample6 phenoB location2 sample7 phenoA location2 sample8 phenoA location2
I have analyzed the association between phenoA and SNP sites
however, I want to analyze the association between phenoA and SNP sites of samples only in location1 and location2 separately. Is --within argument in PLINK useful in such a situation?
Thanks for help