Difference between revisions of "RAREMETALWORKER SPECIAL TOPICS"
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| + | This page describes how RAREMETALWORKER handles some special cased during analyses. | ||
== Handling Unrelated Individuals == | == 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. | ||
Revision as of 11:12, 14 April 2014
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
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.
