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, 11:11, 14 April 2014
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− | === Handling Unrelated Individuals ===
| + | == Handling Unrelated Individuals == |
| * 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. | | * 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. |
| * 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. | | * 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. |
| * However, when --kinGeno (or --kinFile) is issued, RAREMETALWORKER will estimate genomic relationship matrix from genotypes and use linear mixed model to make proper adjustment. | | * However, when --kinGeno (or --kinFile) is issued, RAREMETALWORKER will estimate genomic relationship matrix from genotypes and use linear mixed model to make proper adjustment. |
| | | |
− | === Missing Data ===
| + | == Missing Data == |
| | | |
| Individuals with missing phenotypes will be excluded from analysis. 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 with missing phenotypes will be excluded from analysis. 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. |