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Jump to navigationJump to search→Stage 1: Local Sites Produce Summary Statistics Using Rare-Metal-Worker
The meta-analysis step (stage 2) requires a very specific set of summary statistics, which includes single-variant test statistics and p-values, as well as the test statistic covariance matrix within a sliding window (default: 1Mb). Shuang Feng, Dajiang Liu, and Goncalo Abecasis at the University of Michigan have developed software specifically for this purpose, called Rare-Metal-Worker. Software and usage instructions to generate necessary single variant statistics is available at [http://genome.sph.umich.edu/wiki/Rare-Metal-Worker Rare-Metal-Worker].If there are installation problems please let Scott know.
The meta-analysis step (stage 2) requires a very specific set of summary statistics, which includes single-variant test statistics and p-values, as well as the test statistic covariance matrix within a sliding window (default: 1Mb). Shuang Feng, Dajiang Liu, and Goncalo Abecasis at the University of Michigan have developed software specifically for this purpose, called Rare-Metal-Worker. Software and usage instructions to generate necessary single variant statistics is available at [http://genome.sph.umich.edu/wiki/Rare-Metal-Worker Rare-Metal-Worker].If there are installation problems please let Scott know.
'''NOTE:''' It is essential that, after each trait has been log-transformed (except for CPD) and corrected for covariates, the residuals are inverse normalized, and then association testing is conducted, in that order. The Rare-Metal-Worker software has this functionality when you jointly specify
'''NOTE:''' It is essential that analysis proceeds in the following order. For CPD, please bin quantitative responses and correct for covariates to obtain residuals. For all other phenotypes, please left-anchor responses at 1, log-transform, and then correct for covariates. In this way we will obtain residualized phenotypes ready for analysis with Rare-Metal-Worker. These steps are probably easier to do in your software of choice.
Now, using the residualized phenotypes in a .ped file please specify the --makeResiduals and --inverseNormalize options. These will correct for the intercept and then inverse-normalize the phenotype prior to conducting association tests.
==== Submitting Results for Meta-Analysis ====
==== Submitting Results for Meta-Analysis ====
