GCTAx: Extended GCTA Analysis:
Gregory Carey

Tony Blair



GCTAx is a series of R functions designed to extend Yang et al.'s Genome Complex Trait analysis (GCTA) to problems that can cannot be fitted using the Yang program. For example, one can perform GCTA meta-analysis, analyze more than two phenotypes, fit GE moderation models with a continuous moderator, etc.


GCTAx can be used as a data management tool for manipulating and structuring data prior to GCTA analysis. Once that is done, models can be fitted to the data using either GCTAx or OpenMx. In either case, a user must write the model and in the case of GCTAx, write a function in R or subroutine in c or fortran that calculates and returns a function value for a sample. Although the R function sounds ominous, there are R functions that can assist you. For example, with these functions it only takes 7 R statements to write a function that calculates the log likelihood for a 20 parameter model on height and weight in females and males.


Because you write the function, GCTAx is very flexible. You can fit means or (recommended) center the data to avoid fitting extra parameters. You can use full information maximum likelihood, resrtricted maximum likelihood with mixed fixed and random effects, or least squares. See the "hints" section of the manual.

To use GCTAx:

(1) Download the files here.

(2) Unzip the download. (You may have to fiddle with this in Windows),

(3) GCTAx_beta_0.0.1: Contains the source to the R functions

(4) testData1: code to generate and fit models for a simple meta-analysis

(5) testData2: height and weight in males and females

(6) testData3: example of GCTAx_createOpenMxModel

(7) Look at the manual, section Hints --> Getting started