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* there are ~1000 markers included in the VCF file.
* there are ~1000 markers included in the VCF file.
* To analyze this sample accounting for hidden relatedness, an empirical kinship should be calculated.
* To analyze this sample accounting for hidden relatedness, an empirical kinship should be calculated.
* By using the following command, covariates are adjusted and residuals are inverse normalized on the fly.
* By using the following command, covariates are adjusted and residuals are inverse normalized.
$yourPath/bin/raremetalworker --ped rmw_tutorial/inputfiles/example1.ped --dat rmw_tutorial/inputfiles/example1.dat --vcf rmw_tutorial/inputfiles/example1.vcf.gz --prefix rmw_tutorial/output/example1 --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno
* The second sample can also be analyzed in the same fashion using the following command:
* The second sample can also be analyzed in the same fashion using the following command:
$yourPath/bin/raremetalworker --ped $yourLocalPath/rmw_tutorial/inputfiles/example2.ped --dat $yourLocalPath/rmw_tutorial/inputfiles/example2.dat --vcf
$yourPath/bin/raremetalworker --ped $yourLocalPath/rmw_tutorial/inputfiles/example2.ped --dat $yourLocalPath/rmw_tutorial/inputfiles/example2.dat --vcf
* After the two runs are finished, you will see the following output files under your current path:
* After the two runs are finished, you will see the following output files under your current path:
example1.singlevar.score.txt
example1.QT1.singlevar.score.txt
example1.singlevar.cov.txt
example1.QT1.singlevar.cov.txt
example2.singlevar.score.txt
example2.QT1.singlevar.score.txt
example2.singlevar.cov.txt
example2.QT1.singlevar.cov.txt
* The output file ending with singlevar.score.txt includes summary statistics of single marker score tests.
* The output file ending with singlevar.score.txt includes summary statistics of single marker score tests.
* The output file ending with singlevar.cov.txt includes summary variance-covariance matrices of score statistics.
* The output file ending with singlevar.cov.txt includes summary variance-covariance matrices of score statistics.
