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Revision as of 22:18, 29 August 2010
, 22:18, 29 August 2010Created page with '== Association with MACH output == After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in un…'
== Association with MACH output ==
After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.
You will need a *.ped and *.dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] that contain the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file)
mach2dat -p myfile.ped -d myfile.dat --infofile myfile.mlinfo --dosefile myfile.mldose
where myfile.mlinfo and myfile.mldose are the MACH output files.
You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.
*Please note that mach2dat analyze only unrelated samples. If you input family relationship, those will be ignored.
If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]
After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.
You will need a *.ped and *.dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] that contain the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file)
mach2dat -p myfile.ped -d myfile.dat --infofile myfile.mlinfo --dosefile myfile.mldose
where myfile.mlinfo and myfile.mldose are the MACH output files.
You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.
*Please note that mach2dat analyze only unrelated samples. If you input family relationship, those will be ignored.
If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]
