Phenix

In Greek mythology, a phoenix or phenix (Greek: φοῖνιξ phoinix; Latin: phoenix, phœnix, fenix) is a long-lived bird that is cyclically regenerated or reborn

PHENIX (PHENotype Imputation eXpediated) is the name of our method for imputing missing phenotypes where samples have an arbitrary level of relatedness. The method can also be used for dimensionality reduction of multiple traits in related samples. The resulting latent traits can be tested as phenotypes, and can result in an increase in power.

The method is described in detail in this paper

Andrew Dahl, Valentina Iotchkova, Amelie Baud, Åsa Johansson, Ulf Gyllensten, Nicole Soranzo, Richard Mott, Andreas Kranis, Jonathan Marchini. A multiple phenotype imputation method for genetic studies. Nature Genetics

We have made available an R package that implements this method for non-commercial use only.

Please read this licence here

The R package and manual can be downloaded from this Dropbox folder.

A related paper on modelling multiple phenotypes is

Andy Dahl, Victoria Hore, Valentina Iotchkova, Jonathan Marchini (2013). Network inference in matrix-variate Gaussian models with non-independent noise.