RAREMETALWORKER SPECIAL TOPICS: Difference between revisions

From Genome Analysis Wiki
Jump to navigationJump to search
← Older editNewer edit →
Shuang Feng (talk | contribs)
2,004 edits
Undo revision 10107 by Shuang Feng (talk)
Shuang Feng (talk | contribs)
2,004 edits
No edit summary
Line 1: Line 1:
This page describes how RAREMETALWORKER handles some special cased during analyses.
This page describes how [[RAREMETALWORKER]] handles some special cased during analyses.


== Unrelated Individuals ==
== Unrelated Individuals ==
Line 14: Line 14:
== Analyzing Chromosome X==
== 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.
* Special cares only needs
* 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.

Revision as of 11:21, 14 April 2014

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

  • Special cares only needs
Retrieved from "http://genome.sph.umich.edu/w/index.php?title=RAREMETALWORKER_SPECIAL_TOPICS&oldid=10111"