RAREMETALWORKER SPECIAL TOPICS: Difference between revisions
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RAREMETALWORKER calculates, together with key formulae. | 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. | |||
===NOTATIONS=== | ===NOTATIONS=== | ||
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== Missing Data == | == Missing Data == | ||
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Revision as of 11:18, 14 April 2014
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.
NOTATIONS
We use the following notations to describe our methods:
This page describes how RAREMETALWORKER handles some special cased during analyses.
- 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.
Missing Data
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