RAREMETALWORKER SPECIAL TOPICS

This page describes how RAREMETALWORKER handles some special cased during analyses.

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.

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.

Analyzing Chromosome X

• 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.