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, 13:06, 26 August 2013
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| == Key Features == | | == Key Features == |
− | '''rareMETAL''' has the following features: | + | '''RAREMETAL''' has the following features: |
− | * '''rareMETAL''' performs gene-based or region-based meta analysis using Burden tests with the following methods: CMC_counts, Madsen-Browning, SKAT, and Variable Threshold. | + | * '''RAREMETAL''' performs gene-based or region-based meta analysis using Burden tests with the following methods: CMC_counts, Madsen-Browning, SKAT, and Variable Threshold. |
− | * '''rareMETAL''' performs single variant metal-analysis by default. | + | * '''RAREMETAL''' performs single variant metal-analysis by default. |
− | * '''rareMETAL''' allows customized groups of variants to be tested. | + | * '''RAREMETAL''' allows customized groups of variants to be tested. |
− | * '''rareMETAL''' allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis. | + | * '''RAREMETAL''' allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis. |
− | * '''rareMETAL''' generate QQ plots and manhattan plots by default. | + | * '''RAREMETAL''' generate QQ plots and manhattan plots by default. |
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| == Brief Description == | | == Brief Description == |
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− | '''rareMETAL''' is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data. '''rareMETAL''' takes summary statistics and LD matrices generated by [[Rare-Metal-Worker|'''rareMetalWorker''']], handles related and unrelated individuals, and supports both single variant and burden meta-analysis. '''rareMETAL''' generated high quality plots by default and has options that allow users to build reports at different levels. | + | '''RAREMETAL''' is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data. '''RAREMETAL''' takes summary statistics and LD matrices generated by [[Rare-Metal-Worker|'''RAREMETALWORKER''']], handles related and unrelated individuals, and supports both single variant and burden meta-analysis. '''RAREMETAL''' generated high quality plots by default and has options that allow users to build reports at different levels. |
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− | '''rareMETAL''' 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. | + | '''RAREMETAL''' 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. |
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| == Approach == | | == Approach == |
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− | The key idea behind meta-analysis with 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: | + | The key idea behind meta-analysis with 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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