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− | == Brief Introduction== | + | == Handling Unrelated Individuals== |
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− | [[RAREMETALWORKER]] generates single variant association test statistics for a single study prior to meta-analysis. This page provides a brief description of the statistics that
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− | RAREMETALWORKER calculates, together with key formulae.
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− | == Key Statistics for Analysis of Single Study ==
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− | ===NOTATIONS===
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− | We use the following notations to describe our methods:
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− | This page describes how RAREMETALWORKER handles some special cased during analyses.
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− | == 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. |
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| == Missing Data == | | == 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. | | 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. |