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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]
== Key Instructions ==
== Key Instructions ==
Reformat the phenotype files in the same order of .tfam files. The phenotype file has three entries at each line, FAMID, INDID, and phenotype values. Missing phenotype values should be represented as "NA". It is simpler to regress out the covariates when generating the phenotypes, but it is possible to simultaneously adjust for covariates.
Reformat the phenotype files in the same order of .tfam files. The phenotype file has three entries at each line, FAMID, INDID, and phenotype values. Missing phenotype values should be represented as "NA". It is simpler to regress out the covariates when generating the phenotypes, but it is possible to simultaneously adjust for covariates.
Sample lines of phenotype files. (tab or space delimited)
Sample lines of phenotype files. (tab or space delimited)
859811 859811 0.609109817670387
862311 862311 -0.0735227335684144
862311 862311 -0.0735227335684144
864111 864111 -0.210247209814720
864111 864111 -0.210247209814720
Q. Which allele is effect allele?
Q. Which allele is effect allele?
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)
=== Support for VCF format and Gene-level Burden Test ===
=== Support for VCF format and Gene-level Burden Test ===
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.
=== Encoding Case-control Phenotypes ===
Q. I would like to run EMMAX for case-control phenotypes. How can I encode the phenotypes?
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).
=== IBS matrix or BN matrix? ===
Q. Between IBS and BN matrix, which one is preferred?
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.
=== NaN in the kinship file ===
Q. I am observing a series of -nan in the kinship matrix. What is the problem?
A. Most likely, monomorphic SNPs would create such a problem. Typically, MAF threshold such as 1% is used.
=== Citing EMMAX ===
=== Citing EMMAX ===
Q. How can I cite EMMAX if I used it?
Q. How can I cite EMMAX if I used it in my research?
A. Please see http://www.ncbi.nlm.nih.gov/pubmed/20208533, or copy the line below.
A. Please see http://www.ncbi.nlm.nih.gov/pubmed/20208533, or copy the line below.
