Efficient Mixed-Model Association eXpedited (EMMAX)

The current version of EMMAX release is beta version which support PLINK's transposed PED file. A complete version of the software will be appearing soon.

1. Use PLINK software to transpose your genotype files (bed or ped format) to tped/tfam format by running

% plink --bfile [bed_prefix] (or --file [ped_prefix]) --recode12 --output-missing-genotype 0 --transpose --out [tped_prefix]

2. 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.

59811	859811	0.609109817670387
862311	862311	-0.0735227335684144
864111	864111	-0.210247209814720
865211	865211	-0.154258680369780
875511	875511	0.239822160194388
880111	880111	0.287436401143001
880811	880811	NA
881511	881511	0.114872064616424
88211	88211	-0.0165529689285573

3. Create kinship matrix (IBS or BN) using emmax-kin. Make sure that both .tped and .tfam file exist with the same prefix.

IBS matrix
% emmax-kin -v -h -s -d 10 [tped_prefix] (will generate [tped_prefix].hIBS.kinf)

BN matrix
% emmax-kin -v -h -d 10 [tped_prefix] (will generate [tped_prefix].hBN.kinf)

4. Run EMMAX with the phenotype, tped/tfam files, and the kinship files as follows.

% emmax -v -d 10 -t [tped_prefix] -p [pheno_file] -k [kin_file] -o [out_prefix]

This will generate the following files:
* [out_prefix].rem : REML output. The last line denotes the pseudo-heritability estimates
* [out_prefix].ps : Each line consist of [SNP ID], [beta], [p-value].

If one wants to adjust for covariates simultanenously, add -c [cov_file] options to the above run, with the covariate file similar to the phenotype files, but allowing multiple columns ( > 3 ). Note that the intercept has to be included, meaning that the third column is recommended to be 1 always, and the covariates needs to be included from the fourth column. The order of the individual IDs should conform to the .tfam files, similar to the phenotype files.

100211 100211 1 2
100611 100611 1 2
100711 100711 1 3
100811 100811 1 4
101611 101611 1 2
101711 101711 1 2

Instructions