Readme

JointGWAS, a package for multivariate Genome Wide Association Studies

Quick start:

Install the package with:

devtools::install_github('ucdavis/JointGWAS',ref = 'master')

JointGWAS needs a kinship matrix among individuals (), and genetic and residual covariance matrices among traits ( and ). You also need a data.frame (data) with a column identifying the genotype (ID), and a matrix of marker genotypes with rownames of the the genotype identifiers.

There are two ways to run the joint GWAS. If your trait data are stacked in a single column (y), use EMMAX_ANOVA. In this case, data also needs an identifier of each trait (Trait).

cholL_Sigma_inv = make_cholL_Sigma_inv(data,
                                       phenoID='y',rowID='ID',columnID='Trait',
                                       covariances = list(list(Row=K,Column=Ghat),
                                                          list(Column=Rhat))
                                       )
results = EMMAX_ANOVA(formula=y~0+Trait+X:Trait,data,markers,'ID',cholL_Sigma_inv,mc.cores=1,verbose=TRUE)

If your trait data are in an matrix (Y), use EMMAX_ANOVA_matrix:

sK = svd(K)
sGR = simultaneous_diagonalize(Ghat,Rhat)
results = EMMAX_ANOVA_matrix(formula=Y~X,data,markers,'ID',svd_matrices = list(sK,sGR),mc.cores = 1,verbose=TRUE)

In both cases, formula is used to specify the linear model to be fit for each marker. The term X is special and reserved for the genotype values of a marker, and will be replaced with the genotype values for each column of markers one-by-one. This means that you cannot have a column X in data. The GWAS functions will extract each term from formula including X and do an F-test for that term using R’s anova function.

The output is a list with 3 elements:

• anova: a data.frame with columns giving the MSE, F-statistics and p-values for the tests on each term in formula including the special variable X. Each row corresponds to a column of markers.

• beta_hats: a matrix of genotype term coefficients. Each column is a specific genotype effect (e.g. for one trait).

• SEs: a matrix of standard errors for each column of beta_hats.

Motivation

Here is a simulation to show how a joint test of association of a marker with either of two traits is more powerful than univariate associations with either trait. In this case, the marker is directly associated only with trait 1, but traits 1 and 2 are correlated:

## [1] "p-values of individual traits"

## [1] 0.03256696 0.61433609

## [1] "pvalue of F-test across both traits"

## [1] 7.46622e-08

While trait 1 is weakly associated with X, the association in the bi-variate space is much stronger.

Mathematical Background

A multivariate genetic association test can be specified as:

where:

• is an matrix of traits

• is an matrix of covariates (e.g. sex, age, environment) with coefficient matrix

• is an matrix of genotype covariates with matrix of genotype effects , and

• is an matrix of residual errors.

In a typical univariate GWAS, is an vector and is a scalar, and the GWAS test is against . Here we generalize this to tests on sets of elements of being all equal 0. For example, if is a vector of genotypes and is a row-vector of genotype effects for each of the traits, we could test against .

An equivalent formulation of this problem is to work with the vectorized form of this equation:

where:

• is the vector formed by stacking the columns of

• is a matrix of covariates with coefficient vector

• is a matrix of genotype covariates with coefficient vector , and

• 

Using this form, we can more flexibly specify and . For example, we could include a main effect for a marker across all traits, a slope of the marker effects across traits based on a covariate, and trait-specific deviations from the mean marker effects.

Accounting for correlated observations and traits

In most GWAS applications it is necessary to account for population structure and general relatedness among the observations using a kinship matrix. The solution is to include a structured error term: where , is an genomic relationship matrix among the observations, and the two variance components are typically estimated by REML. This is the typical linear mixed model GWAS.

In the multivariate GWAS context we need to generalize this structured error term to account for both genomic relationships among observations and correlations among the traits. A multivariate extension to mixed model GWAS sets where and , with and covariance matrices representing the covariation of the genetic effects and microenvironmental residuals, respectively. and can both be estimated by REML.

Strategies for computational efficiency in GWAS

Once the estimates of the variance components are available, solutions and tests for can by found by generalized least squares. However, the REML solutions for these parameters are computationally costly. EMMA, FaSTLMM and GEMMA showed how rotations of the model based on the SVD of can vastly speed up the calculations of the REML solutions, which makes exact GWAS solutions possible. GEMMA was extended to multivariate GWAS, but is limited to a small number of traits and is considerably more computationally demanding than univariate GEMMA.

Alternatively, EMMAX and GridLMM showed that approximate solutions for the variance components are generally sufficient for accurate GWAS, particularly when the effect of any specific marker are small. Using EMMAX instead of EMMA means finding REML solutions for the variance components in a reduced model without the term, and then solving for conditional on these estimates using generalized least squares. In this way the variance components do not need to be re-estimated for each marker. XX proved that EMMAX as a GWAS method is mathematically equivalent to GBLUP as a genomic prediction method if for markers, and the marker tests and effect sizes can be extracted from the GBLUP solution.

We uses these latter results to perform approximate multivariate linear mixed model GWAS in JointGWAS. Given estimates and we find solutions and tests for . For computational efficiency we project out from the model first and return estimates and tests for only.

Implementation

As mentioned above, there are two entries into the GWAS functions depending on whether your data is in matrix or vector form. For the same number of traits, the matrix function is much faster. However, it is limited to the case where every trait is measured on every individual. It is also more limited in the types of models that can be fit - models where there are main effects of markers across traits are not currently implemented in the matrix form.

`EMMAX_ANOVA` usage

When each trait is measured on a subset of the individuals (or some trait:individual combinations are missing), `EMMAX_ANOVA` must be used. This is the “long-form” model with trait values stacked in a single column vector.

Start by setting up a data.frame with at minimum a column to identify the genotype (genoypeID) and a column to identify the trait (Trait). You can include other covariates that you would like, for example covariates that differ among the genotypes, among the traits (e.g. if traits are yield in different trials, you could include covariates to describe the trial conditions), and covariates that differ among the observations.

Now, write the model formula for the long-form data. This should include a term for Trait, and a term for marker effects for each trait: X:Trait. Optionally you can include the other covariates and covariate:marker interactions. The simplest model would be:

y~Trait+X:Trait

Note: Remember that X is a special term that can only refer to columns of the marker matrix.

Prepare your marker data in a matrix with individuals as rows and markers as columns. If you include column names, these will be included in the output. Row names are required and much include all levels of data[[genotypeID]]. Note: the marker matrix should have one row for each genotype, even if a genotype is present in multiple rows of data.

Before running the GWAS, we have to prepare the error term. Typically we have a single kinship matrix with a corresponding genetic covariance matrix and a residual covariance matrix . With these, we combine them into the full covariance matrix using the function make_cholL_Sigma() :

cholL_Sigma_inv = make_cholL_Sigma_inv(data,
                                       phenoID='y',rowID='ID',columnID='Trait',
                                       covariances = list(list(Row=K,Column=Ghat),
                                                          list(Column=Rhat))
                                       )

To run this function, we pass our long-form data matrix which includes the phenotype column, the columns of data identifying genotypes (here called rowID) and traits (here called columnID and paired lists of matrices specifying components of the overall covariance. In our typical case we have 2 components, the pair () and the pair ($\mathbf{I},\mathbf{R}$), but it is possible to include more pairs if needed. Note: if either the Row or Column argument of a pair is missing it is assumed to be the identity matrix.

Finally, we can run the GWAS by passing these arguments to the EMMAX_ANOVA function:

results = EMMAX_ANOVA(formula=y~Trait+X:Trait,data,markers,'ID',cholL_Sigma_inv,mc.cores=1,verbose=TRUE)

The mc.cores argument allows the tests to be parallelized over processor cores.

EMMAX_ANOVA_matrix usage

When every trait is measured on every subject, the phenotype data can be arranged into a matrix with no missing values. In this case we can use more efficient calculations.

Start by setting up a data.frame with at minimum a column to identify the genotype (genoypeID). Note: there will be no column for trait here because this data.frame describes the characteristics of each genotype, not each trait.

Form the data into a matrix Y with rows corresponding to the rows of data, and columns as traits. It is also possible to incorporate Y into data and refer to the trait matrix with its trait names in the formula as cbind(trait1,trait2,trait3).

Write the model formula that applies individually to each trait. If you have covariates that describe the genotypes, include these terms. Also include a term for the marker effect on a trait. The simplest model would be:

Y~X

Note: Remember that X is a special term that can only refer to columns of the marker matrix.

Prepare your marker data in a matrix with individuals as rows and markers as columns. If you include column names, these will be included in the output. Row names are required and much include all levels of data[[genotypeID]]. Note: the marker matrix should have one row for each genotype, even if a genotype is present in multiple rows of data.

Before running the GWAS, we have to prepare the error term. Typically we have a single kinship matrix with a corresponding genetic covariance matrix and a residual covariance matrix . We prepare the error term by taking the singular value decompositions of the row and column matrices separately. Note: This only works with two variance components (K + I).

sK = simultaneous_diagonalize(K,diag(1,nrow(data))) # could be replaced with svd(K)
sGR = simultaneous_diagonalize(Ghat,Rhat)

Finally, we can run the GWAS by passing these arguments to the EMMAX_ANOVA_matrix function:

results = EMMAX_ANOVA_matrix(formula=Y~X,data,markers,'ID',svd_matrices = list(sK,sGR),mc.cores = 1,verbose=TRUE)

There is one additional optional argument for `EMMAX_ANOVA_matrix`: cis_markers. This is an argument specifically for eQTL analyses where for specific markers you can remove specific traits from the overall F-test of joint marker effects. Since cis-eQTL are so common, if a marker is in cis to one of the genes in Y, a significiant F-test for the association between this marker and any gene in Y is not particularly interesting because it is likely just a cis effect on the local gene. But we may still want to know if this marker is a QTL for any other gene in Y. In this case we can simply pull out the nearby gene(s) from the F-test and perform the test between the marker and the remaining genes (accounting for covariances among all genes in Y). cis_markers is a list with p elements where the ith element is a vector of columns of Y that should be removed from the F-test for marker i. In this case, the F-test for this marker will have fewer numerator degrees of freedom. The coefficients for the remaining columns of Y will be tested last by anova using R’s default Type I SSs.