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Revision as of 11:11, 14 April 2014
, 11:11, 14 April 2014Created page with "=== 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 --ki..."
=== 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.
* 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.
