how do I create .dat file format for mach2dat software association analysis?
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3.7 years ago
anamaria ▴ 220

Hello,

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?

Thanks
Ana

mach2dat associationanalysis dat • 638 views
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