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| − | <!-- markdown-toc start - Don't edit this section. Run M-x markdown-toc/generate-toc again -->
| + | '''(Updated: January 2015; latest documentation can always be found at: [http://zhanxw.github.io/rvtests/ http://zhanxw.github.io/rvtests/])''' |
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| − | '''Table of Contents'''
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| − | * [[#introduction|Introduction]]<br />
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| − | * [[#download|Download]]<br />
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| − | * [[#quick-tutorial|Quick Tutorial]]
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| − | ** [[#single-variant-tests|Single variant tests]]<br />
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| − | ** [[#groupwise-tests|Groupwise tests]]<br />
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| − | ** [[#related-individual-tests|Related individual tests]]<br />
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| − | ** [[#meta-analysis-tests|Meta-analysis tests]]
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| − | *** [[#dominant-models-and-recessive-models|Dominant models and recessive models]]<br />
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| − | * [[#input-files|Input files]]
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| − | ** [[#genotype-file-vcf|Genotype file (VCF)]]<br />
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| − | ** [[#phenotype-file|Phenotype file]]<br />
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| − | ** [[#covariate-file|Covariate file]]<br />
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| − | ** [[#trait-transformation|Trait transformation]]<br />
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| − | * [[#models|Models]]
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| − | ** [[#single-variant-tests|Single variant tests]]<br />
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| − | ** [[#burden-tests|Burden tests]]<br />
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| − | ** [[#variable-threshold-models|Variable threshold models]]<br />
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| − | ** [[#kernel-models|Kernel models]]<br />
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| − | ** [[#meta-analysis-models|Meta-analysis models]]<br />
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| − | ** [[#utility-models|Utility models]]<br />
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| − | * [[#association-test-options|Association test options]]
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| − | ** [[#sample-inclusionexclusion|Sample inclusion/exclusion]]<br />
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| − | ** [[#variant-site-filters|Variant site filters]]<br />
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| − | ** [[#genotype-filters|Genotype filters]]<br />
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| − | ** [[#handle-missing-genotypes-and-phenotypes|Handle missing genotypes and phenotypes]]<br />
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| − | ** [[#specify-groups-eg-burden-unit|Specify groups (e.g burden unit)]]<br />
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| − | * [[#sex-chromosome-analysis|Sex chromosome analysis]]<br />
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| − | * [[#kinship-generation|Kinship generation]]<br />
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| − | * [[#frequently-asked-questions-faq|Frequently Asked Questions (FAQ)]]<br />
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| − | * [[#feedbackcontact|Feedback/Contact]]
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| − | <!-- markdown-toc end -->
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| − | [https://travis-ci.org/zhanxw/rvtests [[Image:https://travis-ci.org/zhanxw/rvtests.png?branch=master|Build Status]]]
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| − | (Updated: Janurary 2015)
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| | = Introduction = | | = Introduction = |
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| | Rvtests is a collaborative effort by Youna Hu, Bingshan Li, Dajiang Liu. | | Rvtests is a collaborative effort by Youna Hu, Bingshan Li, Dajiang Liu. |
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| − | [https://bitdeli.com/free [[Image:https://d2weczhvl823v0.cloudfront.net/zhanxw/rvtests/trend.png|Bitdeli Badge]]]
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