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[[Category:RAREMETALWORKER]]
This page describes how [[RAREMETALWORKER]] handles some special cased during analyses.
This page describes how [[RAREMETALWORKER]] handles some special cased during analyses.
==Useful Links==
Here are some useful links to key pages:
* The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
* The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']]
* The [[RAREMETALWORKER_command_reference | '''RAREMETALWORKER command reference''']]
* The [[Tutorial:_RAREMETAL| '''RAREMETALWORKER quick start tutorial''']]
* The [[RAREMETAL_FAQ | '''FAQ''']]
== Unrelated Individuals ==
== 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]] 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 ==
== Missing Data ==
* If --makeResiduals is used for adjusting covariates, then individuals with missing covariates will also be excluded.
* 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 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 must be code as 1 and female must 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.
* 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 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.
* 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.
* However, when --kinGeno (or --kinFile) is issued, RAREMETALWORKER will estimate genomic relationship matrix from genotypes and use linear mixed model to make proper adjustment.
* 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 [[RAREMETALWORKER_method | '''method''']].
