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, 11:05, 14 April 2014
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| − | === Handling Unrelated Individuals === | + | ===SPECIAL TOPICS=== |
| − | * To let Rare-Metal-Worker handle unrelated individuals, we just have to code the individuals as unrelated in PED file, or each individual belongs to a unique family. Then Rare-Metal-Worker will take care of the rest. | + | * For special topics such as how RAREMEALWORKER handles missing data, unrelated individuals, markers on chromosomeX, please go to [[RAREMETALWORKER_SPECIAL_TOPICS | '''SPECIAL TOPICS''']]. |
| − | * However, when --kinGenotype is also used, Rare-Metal-Worker will consider them as related and generate kinship matrix from genotypes.
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| − | * An example is shown as following (header is included for illustration purpose, not in real PED file):
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| − | famid pid fid mid sex age trait
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| − | 1 1.1 0 0 1 10 -0.3
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| − | 2 2.1 0 0 1 56 0.0
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| − | 3 3.1 0 0 2 31 0.4
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| − | 4 4.1 0 0 2 23 0.008
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| − | 5 5.1 0 0 2 34 2.35
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| − | === Missing Data ===
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| − | 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.
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| | == Example Command Lines == | | == Example Command Lines == |
