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. | ||
| + | |||
| + | == Analyzing Chromosome X== | ||
| + | |||
| + | * 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. | ||
| + | * However, when --kinGeno (or --kinFile) is issued, RAREMETALWORKER will estimate genomic relationship matrix from genotypes and use linear mixed model to make proper adjustment. | ||
Revision as of 11:20, 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.
Analyzing Chromosome X
- 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.
- However, when --kinGeno (or --kinFile) is issued, RAREMETALWORKER will estimate genomic relationship matrix from genotypes and use linear mixed model to make proper adjustment.
