Download

A PLINK (v1.06) binary file for Unix (32 or 64 bits) with the current implementation of the multivariate test is available below. Binaries for other platforms, the source code and more detailed usage description will be posted shortly.

Unix 64 bits: plink.multivariate

Unix 32 bits: plink.multivariate.32b

To download, you may have to right click on the link and choose "Save Link as..."

After downloading the binary file, give the file permissions with (for 64 bit file in this example):

chmod a+x plink.multivariate

and run as usual for PLINK, with

./plink.multivariate --bfile mydata

If you use this multivariate test in your analysis, please cite the original PLINK paper and Ferreira MA and Purcell SM (2009) A multivariate test of association. Bioinformatics 25(1):132-3.

 

Updates

18 Mar 2009.The source code for the multivariate test (mqfam.cpp) has been updated to use the new Plink1.06 function to read multivariate phenotypes. As a result, the --mqfam analysis should now be called in a slightly different manner, please see the usage section for details. A few new analysis options have also been added: for example, the analysis can now be restricted to only a subset of phenotypes; a file with the individuals used for analysis can now be written out; and printing the phenotype loadings to the output file can now be suppressed. A couple of bugs that resulted in the error "ERROR: Internal error: non-conformable matrices in multMatrix()", should now also be fixed. Common causes of this error were the absence of a main phenotype field in the ped/fam file; a main phenotype field available but with all individuals missing (eg. -9); a SNP that was polymorphic in the overall sample, but monomorphic in the individuals actually used in the mqfam analysis.