Tutorial: RAREMETAL
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Revision as of 19:25, 7 March 2013 by Shuang Feng (talk | contribs) (→STEP 2: Run RareMetalWorker on Individual Studies)
RareMETAL Tutorial
Introduction
In this tutorial, we will show how to run RareMetalWorker and RareMETAL to perform meta analysis using example data sets.
RareMetalWorkr 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 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 example2