RAREMETALWORKER SPECIAL TOPICS: Difference between revisions

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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.
== 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.
* 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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Revision as of 11:19, 14 April 2014

This page describes how RAREMETALWORKER handles some special cased during analyses.

Unrelated Individuals

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.
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