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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:
/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
* 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:
/bin/Rare-Metal-Worker --ped yourInput.ped --dat yourInput.dat --traitName LDL --useCovariates --makeResiduals --inverseNormal
* 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:
/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.)
* 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:
