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RAREMETAL Documentation

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== Key Features ==
'''rareMETALRAREMETAL''' has the following features:* '''rareMETALRAREMETAL''' performs gene-based or region-based meta analysis using Burden tests with the following methods: CMC_counts, Madsen-Browning, SKAT, and Variable Threshold. * '''rareMETALRAREMETAL''' performs single variant metal-analysis by default. * '''rareMETALRAREMETAL''' allows customized groups of variants to be tested.* '''rareMETALRAREMETAL''' allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis.* '''rareMETALRAREMETAL''' generate QQ plots and manhattan plots by default.
== Brief Description ==
'''rareMETALRAREMETAL''' is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data. '''rareMETALRAREMETAL''' takes summary statistics and LD matrices generated by [[Rare-Metal-Worker|'''rareMetalWorkerRAREMETALWORKER''']], handles related and unrelated individuals, and supports both single variant and burden meta-analysis. '''rareMETALRAREMETAL''' generated high quality plots by default and has options that allow users to build reports at different levels.
'''rareMETALRAREMETAL''' is developed by Shuang Feng, Dajiang Liu and Gonçalo Abecasis. A R-package using the same methodology is [[RareMetals|available]]]. Manuscript for this tool is in preparation. Please contact sfengsph at umich dot edu for questions.
== Approach ==
The key idea behind meta-analysis with rareMETAL RAREMETAL is that various gene-level test statistics can be reconstructed from single variant score statistics and that, when the linkage disequilibrium relationships between variants are known, the distribution of these gene-level statistics can be derived and used to evaluate signifi-cance. Single variant statistics are calculated using the Cochran-Mantel-Haenszel method. The main formulae are tabulated in the following:
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