Difference between revisions of "RAREMETALWORKER SPECIAL TOPICS"

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(Analyzing Chromosome X)
(Analyzing Chromosome X)
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== Analyzing Chromosome X==
 
== Analyzing Chromosome X==
  
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* To make sure RAREMETALWORKER analyze chromosome X correctly, '''male has to be code as 1 and female has to be coded as 2''' in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED''']] file.
 
* --xStart and --xEnd options described the start and end position of nonPAR region on chromosome X. The default values are 2699520 and 154931044, according to Human Genome build 19.
 
* --xStart and --xEnd options described the start and end position of nonPAR region on chromosome X. The default values are 2699520 and 154931044, according to Human Genome build 19.
 
* When samples are analyzed as unrelated (no any kind of kinship is used for linear mixed model approach), no special actions needed for analyzing markers on chromosome X.  
 
* When samples are analyzed as unrelated (no any kind of kinship is used for linear mixed model approach), no special actions needed for analyzing markers on chromosome X.  

Revision as of 13:47, 14 April 2014

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

Useful Links

Here are some useful links to key pages:

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.
  • Missing genotypes are imputed using mean genotype of a variant.

Analyzing Chromosome X

  • To make sure RAREMETALWORKER analyze chromosome X correctly, male has to be code as 1 and female has to be coded as 2 in PED file.
  • --xStart and --xEnd options described the start and end position of nonPAR region on chromosome X. The default values are 2699520 and 154931044, according to Human Genome build 19.
  • When samples are analyzed as unrelated (no any kind of kinship is used for linear mixed model approach), no special actions needed for analyzing markers on chromosome X.
  • If you want to use a linear mixed model approach to correct family structure, population structure, or cryptic relatedness, you should issue --vcX option in your command line. This approach will fit a separate linear mixed model using both autosomal kinship matrix and chromosomeX kinship matrix. This approach is believed to have larger power with type I error well controlled.
  • On the other hand, if you want a fast association for chromosome X, another valid approach is to issue --vcX --separateX options. This will initiate fitting a separate linear mixed model using chromosomeX kinship only for analyzing markers on chromosomeX. This approach is expected to be faster than the above option, but with less power, although type I error is also expected to be under control.
  • Male genotypes for variants in nonPAR region are coded to be 0 or 2.
  • If a male is heterozygous in nonPAR region, then the genotype of that male sample is considered missing and will be imputed using mean genotype.
  • If a male has genotype coded as ./x in nonPAR region, then the genotype of that male sample is considered missing and will be imputed using mean genotype.
  • For details of methods analyzing chromosomeX, please refer to method.