Difference between revisions of "RAREMETALWORKER SPECIAL TOPICS"
From Genome Analysis Wiki
Jump to navigationJump to searchShuang Feng (talk | contribs) |
Shuang Feng (talk | contribs) |
||
| Line 1: | Line 1: | ||
| − | == | + | == 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
- 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.
