Difference between revisions of "Tutorial: RAREMETAL"
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==Introduction== | ==Introduction== | ||
In this tutorial, we will show how to run RareMetalWorker and RareMETAL to perform meta analysis using example data sets. | In this tutorial, we will show how to run RareMetalWorker and RareMETAL to perform meta analysis using example data sets. |
Revision as of 19:37, 7 March 2013
Introduction
In this tutorial, we will show how to run RareMetalWorker and RareMETAL to perform meta analysis using example data sets.
RareMetalWorker is the pre-processing tool to analyze data from individual studies and generate summary statistics for further meta analysis using RareMETAL.
RareMETAL is the tool to do gene-level meta analysis.
STEP 1: Install Software and Download Example Data Sets
- If RareMETAL and RareMetalWorker have not been installed on your local computer yet, please follow the following directions for installation. Install RareMetalWorker, Install RareMETAL
- Download the example data set for RareMetalWorker to your local drive: RareMetalWorker example data sets
- Go to your local path where the tar ball was saved then extract
tar xvzf raremetalworker.tutorial.tgz #extract cd rmw_tutorial
- Download the example data set for RareMetal to your local drive: RareMetalWorker example data sets
- Go to your local path where the tar ball was saved then extract
tar xvzf raremetal.tutorial.tgz #extract cd raremetal_tutorial
STEP 2: Run RareMetalWorker on Individual Studies
- The first example has 743 individuals coded as unrelated according to PED file (each person belongs to an individual family).
- there are ~1000 markers included in the VCF file.
- 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.
$yourPath/bin/raremetalworker --ped $yourLocalPath/rmw_tutorial/inputfiles/example1.ped --dat $yourLocalPath/rmw_tutorial/inputfiles/example1.dat --vcf $yourLocalPath/rmw_tutorial/inputfiles/example1.vcf.gz --kinGeno --kinSave --traitName LDL --inverseNormal --makeResiduals --useCovariates --prefix $yourLocalPath/rmw_tutorial/outputfiles/example1
- 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 $yourLocalPath/rmw_tutorial/inputfiles/example2.vcf.gz --kinGeno --kinSave --traitName LDL --inverseNormal --makeResiduals --useCovariates --prefix $yourLocalPath/rmw_tutorial/outputfiles/example2
- After the two runs are finished, you will see the following output files under your current path:
example1.singlevar.score.txt example1.singlevar.cov.txt example2.singlevar.score.txt example2.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.cov.txt includes summary variance-covariance matrices of score statistics.