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, 09:58, 2 February 2017
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| == Download EMMAX == | | == Download EMMAX == |
− | The latest release of EMMAX can be downloaded at [http://www.sph.umich.edu/csg/kang/emmax/download/index.html EMMAX Download Page] | + | The latest release of EMMAX can be downloaded at [http://csg.sph.umich.edu//kang/emmax/download/index.html EMMAX Download Page] |
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| == Key Instructions == | | == Key Instructions == |
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| Q. Which allele is effect allele? | | Q. Which allele is effect allele? |
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− | A. EMMAX simply follows the encoding scheme of .tped file in additive model. So whichever allele encoded as 1 in the .tped file, it will be the effect allele (usually the major allele) | + | A. EMMAX simply follows the encoding scheme of .tped file in additive model. So whichever allele encoded as 2 in the .tped file, it will be the effect allele (usually the major allele) |
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| === Support for VCF format and Gene-level Burden Test === | | === Support for VCF format and Gene-level Burden Test === |
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| A. Use [[EPACTS]] software pipeline for running EMMAX with VCF files, including the implementations of gene-level burden tests. | | A. Use [[EPACTS]] software pipeline for running EMMAX with VCF files, including the implementations of gene-level burden tests. |
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| + | === Encoding Case-control Phenotypes === |
| + | Q. I would like to run EMMAX for case-control phenotypes. How can I encode the phenotypes? |
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| + | A. If you encode case/control to 2/1, you will be able to run case-control analysis. Because EMMAX is based on linear mixed model rather than generalized mixed model, the effect size (beta) would not be meaningful, but the p-values should be reliable (unless case/control counts are highly imbalanced). |
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| + | === IBS matrix or BN matrix? === |
| + | Q. Between IBS and BN matrix, which one is preferred? |
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| + | A. We believe that BN matrix is more robust to construct the empirical kinship matrix. Also we recommend to use call rate 95% threshold and MAF threshold of 0.01 when preparing the data. |
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| + | === NaN in the kinship file === |
| + | Q. I am observing a series of -nan in the kinship matrix. What is the problem? |
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| + | A. Most likely, monomorphic SNPs would create such a problem. Typically, MAF threshold such as 1% is used. |
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| === Citing EMMAX === | | === Citing EMMAX === |