RAREMETALWORKER SPECIAL TOPICS: Difference between revisions

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== Brief Introduction==
== Handling 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.
 
== Key Statistics for Analysis of Single Study ==
 
===NOTATIONS===
 
We use the following notations to describe our methods:
 
 
This page describes how RAREMETALWORKER handles some special cased during 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.  
* 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.  
* 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.
* 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 ==
== 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.
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.

Revision as of 11:17, 14 April 2014

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

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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