Difference between revisions of "RAREMETAL METHOD"

INTRODUCTION

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:

KEY FORMULAE

SKAT META ANALYSIS

Formulae for RAREMETAL
Test Statistics Null Distribution Notation
Single Variant ${\displaystyle T=\sum _{i=1}^{n}{U_{i}}{\bigg /}{\sqrt {\sum _{i=1}^{n}{V_{i}}}}}$ ${\displaystyle T\sim \mathbf {N} (0,1)}$ ${\displaystyle U_{i}{\text{ is the score statistic from study }}i;}$${\displaystyle V_{i}{\text{ is the variance of }}U_{i}.}$
un-weighted Burden ${\displaystyle T_{b}=\sum _{i=1}^{n}{\mathbf {U_{i}} }{\Big /}{\sqrt {\sum _{i=1}^{n}{\mathbf {V_{i}} }}}}$ ${\displaystyle T_{b}\sim \mathbf {N} (0,1)}$ ${\displaystyle \mathbf {U_{i}} {\text{ is the vector of score statistics from study }}i,or}$ ${\displaystyle \mathbf {U_{i}} =\{U_{i1},...,U_{im}\};}$ ${\displaystyle \mathbf {V_{i}} {\text{ is the covariance of }}\mathbf {U_{i}} .}$
Weighted Burden ${\displaystyle T_{wb}=\mathbf {w^{T}} \sum _{i=1}^{n}{\mathbf {U_{i}} }{\bigg /}{\sqrt {\mathbf {w^{T}} \left(\sum _{i=1}^{n}{\mathbf {V_{i}} }\right)\mathbf {w} }}}$ ${\displaystyle T_{wb}\sim \mathbf {N} (0,1)}$ ${\displaystyle \mathbf {w^{T}} =\{w_{1},w_{2},...,w_{m}\}^{T}{\text{ is the weight vector.}}}$
VT ${\displaystyle T_{VT}=\max(T_{b\left(f_{1}\right)},T_{b\left(f_{2}\right)},\dots ,T_{b\left(f_{m}\right)}),{\text{ where}}}$${\displaystyle T_{b\left(f_{j}\right)}={\boldsymbol {\phi }}_{f_{j}}^{\mathbf {T} }\sum _{i=1}^{n}{\mathbf {U_{i}} }{\bigg /}{\sqrt {{\boldsymbol {\phi }}_{f_{j}}^{\mathbf {T} }\left(\sum _{i=1}^{n}{\mathbf {V_{i}} }\right){\boldsymbol {\phi }}_{f_{j}}}}}$ ${\displaystyle \left(T_{b\left(f_{1}\right)},T_{b\left(f_{2}\right)},\dots ,T_{b\left(f_{m}\right)}\right)}$${\displaystyle \sim \mathbf {MVN} \left(\mathbf {0} ,{\boldsymbol {\Omega }}\right){\text{,}}}$${\displaystyle {\text{where }}{\boldsymbol {\Omega _{ij}}}={\frac {{\boldsymbol {\phi }}_{f_{i}}^{T}\left(\sum _{i=1}^{n}{\mathbf {V_{i}} }\right){\boldsymbol {\phi }}_{f_{j}}}{{\sqrt {{\boldsymbol {\phi }}_{f_{i}}^{T}\left(\sum _{i=1}^{n}{\mathbf {V_{i}} }\right){\boldsymbol {\phi }}_{f_{i}}}}{\sqrt {{\boldsymbol {\phi }}_{f_{j}}^{T}\left(\sum _{i=1}^{n}{\mathbf {V_{i}} }\right){\boldsymbol {\phi }}_{f_{j}}}}}}}$ ${\displaystyle {\boldsymbol {\phi }}_{f_{j}}{\text{ is a vector of }}0{\text{s and }}1{\text{s,}}}$ ${\displaystyle {\text{indicating the inclusion of a variant using threshold }}f_{j};}$
SKAT ${\displaystyle \mathbf {Q} =\left(\sum _{i=1}^{n}{\mathbf {U_{i}^{T}} }\right)\mathbf {W} \left(\sum _{i=1}^{n}{\mathbf {U_{i}} }\right)}$ ${\displaystyle \mathbf {Q} \sim \sum _{i=1}^{m}{\lambda _{i}\chi _{1,i}^{2}},{\text{ where}}}$ ${\displaystyle \left(\lambda _{1},\lambda _{2},\dots ,\lambda _{m}\right){\text{ are eigen values of}}}$${\displaystyle \left(\sum _{i=1}^{n}{\mathbf {V_{i}} }\right)^{\frac {1}{2}}\mathbf {W} \left(\sum _{i=1}^{n}{\mathbf {V_{i}} }\right)^{\frac {1}{2}}}$ ${\displaystyle \mathbf {W} {\text{ is a diagonal matrix of weights.}}}$