Mach2dat: Association with MACH output - Revision history

Ylwtx at 02:12, 6 February 2013

2013-02-06T02:12:43Z

← Older revision		Revision as of 22:12, 5 February 2013
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	If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]		If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]

			== where to download ==
			Please go to Li software page [http://www.unc.edu/~yunmli/software.html] for the latest version.

Sannas: /* Association with MACH output */

2010-08-30T02:21:27Z

Association with MACH output

← Older revision		Revision as of 22:21, 29 August 2010
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	*Please note that mach2dat analyze only unrelated samples. If you input family relationship, those will be ignored.		*Please note that mach2dat analyze only unrelated samples. If you input a pedigree with 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]		If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]

Sannas: /* Association with MACH output */

2010-08-30T02:20:56Z

Association with MACH output

← Older revision		Revision as of 22:20, 29 August 2010
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	After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.		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 the .ped and .dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] to specify the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file)		You will need the .ped and .dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] to specify the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file).

			Then, you can run the association using the following command line:


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	You can also add covariates to the phenotype ped and dat files if you want to adjust your test for other variables.		You can also add covariates to the phenotype ped and dat files if you want to adjust your test for other variables.

Sannas: /* Association with MACH output */

2010-08-30T02:20:05Z

Association with MACH output

← Older revision		Revision as of 22:20, 29 August 2010
Line 3:		Line 3:
	After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.		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)		You will need the .ped and .dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] to specify the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file)

Sannas: Created 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…'

2010-08-30T02:18:49Z

Created 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…'

New page

== 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]