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− | === Handling Unrelated Individuals ===
| + | [[Category:RAREMETALWORKER]] |
− | * 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.
| + | This page describes how [[RAREMETALWORKER]] handles some special cased during analyses. |
− | * 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 === | + | ==Useful Links== |
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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. | + | Here are some useful links to key pages: |
| + | * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']] |
| + | * The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']] |
| + | * The [[RAREMETALWORKER_command_reference | '''RAREMETALWORKER command reference''']] |
| + | * The [[Tutorial:_RAREMETAL| '''RAREMETALWORKER quick start tutorial''']] |
| + | * The [[RAREMETAL_FAQ | '''FAQ''']] |
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| + | == 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 |
| + | RAREMETALWORKER calculates, together with key formulae. |
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| + | == 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. |
| + | * Missing genotypes are imputed using mean genotype of a variant. |
| + | |
| + | == Analyzing Chromosome X== |
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| + | * To make sure RAREMETALWORKER analyze chromosome X correctly, '''male must be code as 1 and female must be coded as 2''' in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED''']] file. |
| + | * --xStart and --xEnd options described the start and end position of nonPAR region on chromosome X. The default values are 2699520 and 154931044, according to Human Genome build 19. |
| + | * When samples are analyzed as unrelated (no any kind of kinship is used for linear mixed model approach), no special actions needed for analyzing markers on chromosome X. |
| + | * If you want to use a linear mixed model approach to correct family structure, population structure, or cryptic relatedness, you should issue --vcX option in your command line. This approach will fit a separate linear mixed model using both autosomal kinship matrix and chromosomeX kinship matrix. This approach is believed to have larger power with type I error well controlled. |
| + | * On the other hand, if you want a fast association for chromosome X, another valid approach is to issue --vcX --separateX options. This will initiate fitting a separate linear mixed model using chromosomeX kinship only for analyzing markers on chromosomeX. This approach is expected to be faster than the above option, but with less power, although type I error is also expected to be under control. |
| + | * Male genotypes for variants in nonPAR region are coded to be 0 or 2. |
| + | * If a male is heterozygous in nonPAR region, then the genotype of that male sample is considered missing and will be imputed using mean genotype. |
| + | * If a male has genotype coded as ./x in nonPAR region, then the genotype of that male sample is considered missing and will be imputed using mean genotype. |
| + | * For details of methods analyzing chromosomeX, please refer to [[RAREMETALWORKER_method | '''method''']]. |