Difference between revisions of "RAREMETALWORKER SPECIAL TOPICS"
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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. | ||
| + | * Missing genotypes are imputed using mean genotype of a variant. | ||
== Analyzing Chromosome X== | == Analyzing Chromosome X== | ||
| − | * | + | * --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. | ||
Revision as of 11:34, 14 April 2014
This page describes how RAREMETALWORKER handles some special cased during analyses.
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.
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
- --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.
