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RAREMETALWORKER SPECIAL TOPICS (view source)

Revision as of 11:21, 14 April 2014

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This page describes how RAREMETALWORKER handles some special cased during analyses.
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This page describes how [[RAREMETALWORKER]] handles some special cased during analyses.
    
== Unrelated Individuals ==
 
== Unrelated Individuals ==
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== Analyzing Chromosome X==
 
== Analyzing Chromosome X==
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* 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.
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* Special cares only needs
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* 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.
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* However, when --kinGeno (or --kinFile) is issued, RAREMETALWORKER will estimate genomic relationship matrix from genotypes and use linear mixed model to make proper adjustment.
 
Shuang Feng
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