Entering edit mode
2.5 years ago
anamaria ▴ 180
I am planning to run
mach2dat -p myfile.ped -d myfile.dat --infofile myfile.mlinfo --dosefile myfile.mldose
my question is how to format .dat file in order to include pheno information?
I was running imputation with Mach1 using .dat file that looked like this:
A disease-dummy M2 rs3094315 M2 rs2980300 M2 rs4075116 M2 rs10907175 ...
but how do I include pheno information here for my case control study?
for plink my pheno file for LASER2 as pheno variable looks like this:
FID IID LASER2 fam0110 G110 2 fam0113 G113 2 fam0114 G114 2 fam0117 G117 1
so from here we see that subject: fam0110 G110 is case and fam0117 G117 is control
how do I put this information about pheno into mach2dat?