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Tutorial: RAREMETAL (view source)

Revision as of 18:26, 14 August 2013

912 bytes removed ,  18:26, 14 August 2013
→‎STEP 2: Run RareMetalWorker on Individual Studies
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   cd raremetal_tutorial
 
   cd raremetal_tutorial
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==STEP 2: Run RareMetalWorker on Individual Studies==
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==STEP 2: Analyze individual samples using RAREMETALWORKER==
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===Example 1===
      
* The first example has 743 individuals coded as unrelated according to PED file (each person belongs to an individual family).
 
* The first example has 743 individuals coded as unrelated according to PED file (each person belongs to an individual family).
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* The command above allows you to estimate relatedness according to common variants genotypes with good variant calling quality, adjust for covariates, quantile normalize the residuals before further association analysis of trait QT1. The following output are generated:
 
* The command above allows you to estimate relatedness according to common variants genotypes with good variant calling quality, adjust for covariates, quantile normalize the residuals before further association analysis of trait QT1. The following output are generated:
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  raremetalworker/yourprefix.example1.QT1.singlevar.score.txt (## association results, QC statistics, Genomic control, etc.)
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  raremetalworker/yourprefix.example1.QT1.singlevar.score.txt (## summary statistics, single variant association results, QC statistics, Genomic control, etc.)
 
  raremetalworker/yourprefix.example1.QT1.singlevar.cov.txt (## covariance matrices of score statistics)
 
  raremetalworker/yourprefix.example1.QT1.singlevar.cov.txt (## covariance matrices of score statistics)
 
  raremetalworker/yourprefix.example1.plots.pdf (## QQ plots and manhattan plots)
 
  raremetalworker/yourprefix.example1.plots.pdf (## QQ plots and manhattan plots)
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   $yourpathforRAREMETALWORKER/bin/raremetalworker  --ped example2.ped --dat example2.dat --vcf example2.vcf.gz
 
   $yourpathforRAREMETALWORKER/bin/raremetalworker  --ped example2.ped --dat example2.dat --vcf example2.vcf.gz
 
                                 --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix yourprefix.example2
 
                                 --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix yourprefix.example2
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===Example 2===
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* The second sample can also be analyzed in the same fashion using the following command:
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  $yourPath/bin/raremetalworker --ped $yourLocalPath/rmw_tutorial/inputfiles/example2.ped --dat $yourLocalPath/rmw_tutorial/inputfiles/example2.dat --vcf 
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        $yourLocalPath/rmw_tutorial/inputfiles/example2.vcf.gz --kinGeno --kinSave --traitName LDL --inverseNormal --makeResiduals --useCovariates
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        --prefix $yourLocalPath/rmw_tutorial/outputfiles/example2
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* After the two runs are finished, you will see the following output files under your current path:
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  example1.QT1.singlevar.score.txt
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  example1.QT1.singlevar.cov.txt
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  example2.QT1.singlevar.score.txt
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  example2.QT1.singlevar.cov.txt
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* The output file ending with singlevar.score.txt includes summary statistics of single marker score tests.
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* The output file ending with singlevar.cov.txt includes summary variance-covariance matrices of score statistics.
      
==STEP 3: Run RareMETAL to do Meta Analysis==
 
==STEP 3: Run RareMETAL to do Meta Analysis==
Shuang Feng
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/8153"

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