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, 16:31, 18 November 2012
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| === Related individuals === | | === Related individuals === |
− | * When you have genotype stored in ped file and dat file, and want to use pedigree kinship: | + | * When you have genotype stored in ped file and dat file, and want to use pedigree kinship and inverse normalize traits before adjusting any covariates and doing analysis: |
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− | /bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --traitName LDL | + | /bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --traitName LDL --inverseNormal --useCovariates |
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| + | * When you have genotype stored in ped file and dat file, and want to use pedigree kinship and adjust covariates before inverse normalizing the residuals and doing further analysis: |
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| + | /bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --traitName LDL --useCovariates --makeResiduals --inverseNormal |
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| * When you have genotype stored in ped file and dat file, and want to use kinship generated from genotypes: | | * When you have genotype stored in ped file and dat file, and want to use kinship generated from genotypes: |
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− | /bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --kinGeno --kinSave --traitName LDL (--kinSave allows you to save kinship matrix for future use.) | + | /bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --kinGeno --kinSave --traitName LDL (--kinSave allows you to save kinship matrix for future use; it is optional.) |
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| * When you have genotype stored in vcf file and want to use pedigree kinship: | | * When you have genotype stored in vcf file and want to use pedigree kinship: |