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| | * If --makeResiduals is used for adjusting covariates, then individuals with missing covariates will also be excluded. | | * If --makeResiduals is used for adjusting covariates, then individuals with missing covariates will also be excluded. |
| | * Individuals that are not genotyped will also be excluded from analyses. | | * Individuals that are not genotyped will also be excluded from analyses. |
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| − | == Handling Unrelated Individuals==
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| − | * When each individual has a different famid from each other, or each sample is coded to have different families, and --kinGeno (or --kinFile) option is not issued, RAREMETALWORKER consider the samples as unrelated. No cryptic relationship or population structure will be adjusted in this situation.
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| − | * The easiest way to code the samples as unrelated is to let famid (the first column) the same as the sample ID (the second column) in PED file.
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| − | * However, when --kinGeno (or --kinFile) is issued, RAREMETALWORKER will estimate genomic relationship matrix from genotypes and use linear mixed model to make proper adjustment.
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| − | == Missing Data ==
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