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Revision as of 21:33, 6 September 2013
, 21:33, 6 September 2013→Stage 1: Local Sites Produce Summary Statistics Using Rare-Metal-Worker
=== Stage 1: Local Sites Produce Summary Statistics Using Rare-Metal-Worker ===
=== 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.
Rare-Metal-Worker works best, IMHO, when coding the genotype files as VCF. There are several ways to convert to vcf, including PLINK/SEQ and also WDIST (https://www.cog-genomics.org/wdist/).
'''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 Pack Years, Age of Initiation, and Drinks Per Week, please left-anchor responses at 1, log-transform, and then correct for covariates to obtain residuals. 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.
'''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 Pack Years, Age of Initiation, and Drinks Per Week, please left-anchor responses at 1, log-transform, and then correct for covariates to obtain residuals. 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.
