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, 00:21, 11 December 2012
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| * When you have genotype stored in ped file and dat file, and want to use pedigree kinship and inverse normalize trait values before adjusting any covariates and doing analysis: | | * When you have genotype stored in ped file and dat file, and want to use pedigree kinship and inverse normalize trait values before adjusting any covariates and doing analysis: |
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− | /bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --traitName LDL --inverseNormal --useCovariates | + | /bin/raremetalworker --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: | | * 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 | + | /bin/raremetalworker --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; it is optional.) | + | /bin/raremetalworker --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: |
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− | /bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz | + | /bin/raremetalworker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz |
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| * When you have genotype stored in vcf file and want to use kinship generated from genotype: | | * When you have genotype stored in vcf file and want to use kinship generated from genotype: |
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− | /bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz --kinGeno --kinSave (--kinSave allows you to save kinship matrix for future use.) | + | /bin/raremetalworker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz --kinGeno --kinSave (--kinSave allows you to save kinship matrix for future use.) |
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| === Unrelated individuals === | | === Unrelated individuals === |