# Genetic Correlation of Two Traits using GBLUP¶

## Performing GBLUP Analysis¶

The Genetic Correlation of Two Traits using the GBLUP method performs a bivariate REML analysis on two selected traits to estimate the genetic variance of each trait and the genetic covariance between two traits that can be captured by all SNPs.

Note

This method uses (with a genotypic spreadsheet) or assumes (with a numerically recoded spreadsheet) an additive genetic model.

See *Genetic Correlation Using GBLUP* for more information.

## Options¶

**Computations**: The default computation for genetic correlation includes the residual covariance term as a variance component.*Exclude the residual covariance from computations*: Checking this box excludes the residual covariance term from the computations. This may help convergence in certain cases. (See*Genetic Correlation Using GBLUP*.)

**Impute missing genotypic data as**: Missing genotypic data can be imputed by either of the following methods:*Homozygous major allele*: All missing genotypic data will be recoded to 0.*Numerically as average value*: All missing genotypic data will be recoded to the average of all non-missing genotype calls (using the additive model).Note

If

**Correct for Gender**(see below) is also selected, and there is non-missing data for both males and females in a given marker, averages for males and females will be computed and used separately.

**Correct for Gender**: Assumes the column is coded as if the male were homozygous for the X-Chromosome allele in question. Uses the [Taylor2013] gender-correction algorithm. (See*Correcting the GRM for Gender Using Overall Normalization*and*Correcting the GRM for Gender Using Normalization by Individual Marker*.) Two values of the ASE are output, one for each gender.**Choose Sex Column:**Choose the spreadsheet column that specifies the gender of the sample. This column may either be categorical (“M” vs. “F”) or binary (0 = male, 1 = female).**Chromosome that is hemizygous for males:**Usually the X Chromosome, which is the default.

**Use Pre-Computed Genomic Relationship Matrix**: To use, check this option, then click on**Select Sheet**and select the genomic relationship matrix spreadsheet from the window that is presented. To be valid, this spreadsheet must follow the rules outlined in*Precomputed Kinship Matrix Option*.Note

When using a pre-computed genomic relationship matrix, the matrix and the scaling factor are re-calculated from the genotypic data being used for this analysis.

**Correct for Additional Covariates**: Allows additional fixed effects to be added to this model from columns of this spreadsheet. Fixed effect covariates can be binary, integer, real-valued, categorical or (if actual genotypic data rather than recoded genotypic data is being used for the analysis) genotypic. In all cases, if a marker is used as an additional fixed effect, it will not be included in the analysis in any other way. To begin, check this option, then click on**Add Columns**to get a choice of spreadsheet columns to use.

## GBLUP Correlation Output¶

### The Variance Components¶

As documented in *Genetic Correlation Using GBLUP*, genetic
correlation always involves the following variance components:

V(G1)() Variance of due to random effectsV(G2)() Variance of due to random effectsC(G12)() Covariance between and due to random effectsV(E1)() Error variance forV(E2)() Error variance for

and, if **Exclude the residual covariance from computations** is
unchecked,

C(E12)() (Residual) covariance of and due to error terms.

### Spreadsheet Output¶

The following two spreadsheets will always be created:

GBLUP estimates by sample: This spreadsheet, which contains a row for each sample, contains the following:

A column for each of the two phenotypes

For each phenotype and for each variance component , two columns, one containing the

Gammavector related to phenotype and random effect (or correlation term or error term) , and the other containing theRandom effectrelated to phenotype and random effect (or correlation term or error term) .The

GammaandRandom effectfor phenotype 1 and for phenotype 2 for variance component are defined byand

where matrix is defined in

Finding the Variance Components Using the Average Information (AI) Technique, and can mean any of , , , , , or . (SeeGenetic Correlation Using GBLUP.)For example, suppose that Phenotype 1 is called

PhenAand that Phenotype 2 is calledPhenB. The columns that this spreadsheet will display will then be:

Phenotype 1: PhenAPhenA’s valuesPhenotype 2: PhenBPhenB’s valuesGamma for PhenA from V(G1)The Gamma value forPhenAfor variance componentV(G1)Random effect for PhenA from V(G1)ThePhenArandom effect from variance componentV(G1)Gamma for PhenB from V(G1)The Gamma value forPhenBfor variance componentV(G1)Random effect for PhenB from V(G1)ThePhenBrandom effect from variance componentV(G1)Gamma for PhenA from V(G2)The Gamma value forPhenAfor variance componentV(G2)Random effect for PhenA from V(G2)Etc....Gamma for PhenB from V(G2)Random effect for PhenB from V(G2)Gamma for PhenA from C(G12)Random effect for PhenA from C(G12)Gamma for PhenB from C(G12)Random effect for PhenB from C(G12)Gamma for PhenA from V(E1)Random effect for PhenA from V(E1)Gamma for PhenB from V(E1)Random effect for PhenB from V(E1)Gamma for PhenA from V(E2)Random effect for PhenA from V(E2)Gamma for PhenB from V(E2)Random effect for PhenB from V(E2)and, if

Exclude the residual covariance from computationsis unchecked,

Gamma for PhenA from C(E12)Random effect for PhenA from C(E12)Gamma for PhenB from C(E12)Random effect for PhenB from C(E12)

GBLUP estimates by marker: This spreadsheet, which contains a row for every marker, contains the following columns for each phenotype and for each variance component :

A column for the GBLUP estimates of the allele substitution effect (ASE) by marker relating to phenotype and random effect (or correlation term or error term) .

Note

If

Normalize by Individual Markerhas been used, the actual ASE is found by taking the result as calculated above and dividing its -th element by the factor , where and are the major and minor allele frequencies for marker , respectively.If gender correction is applied, separate columns for the ASE will be output for both males and females for each phenotype and for each random effect (or correlation term or error term) .

For example, suppose that Phenotype 1 is called

PhenAand that Phenotype 2 is calledPhenB. Further suppose that no gender correction is applied. The columns that this spreadsheet will display will then be:

Allele substitution effect (ASE) V(G1) (PhenA)The allele substitution effect for each marker relating to phenotypePhenAand random effectV(G1).ASE V(G1) (PhenB)The allele substitution effect for each marker relating to phenotypePhenBand random effectV(G1).ASE V(G2) (PhenA)The allele substitution effect for each marker relating to phenotypePhenAand random effectV(G2).ASE V(G2) (PhenB)Etc....ASE C(G12) (PhenA)ASE C(G12) (PhenB)ASE V(E1) (PhenA)ASE V(E1) (PhenB)ASE V(E2) (PhenA)ASE V(E2) (PhenB)and, if

Exclude the residual covariance from computationsis unchecked,

ASE C(E12) (PhenA)ASE C(E12) (PhenB)The marker map will be applied to this spreadsheet.

### Node Change Log Output¶

The following will be output to the node change log of each spreadsheet (in addition to the options used and the summary statistics of numbers of records processed, etc.):

The variances for the full model. (This is the only model analyzed by the Genetic Correlation feature.)

First, the number of iterations required for convergence and the log(likelihood) for this model are output.

Then, a table is output containing columns for the description of (

*Source*), the value of (*Variance*), and the standard error (*SE*) of- Each variance component, including error components and covariance components
*Vp1*(), the sum of the variance components for the first phenotype . These components are*V(G1)*() and*V(E1)*().*Vp2*(), the sum of the variance components for the second phenotype . These components are*V(G2)*() and*V(E2)*().- Random-effect variance component
*V(G1)*() divided by - Random-effect variance component
*V(G2)*() divided by

The Genetic Correlation

*rG*(and its standard error).The Genetic Correlation is defined as

or, using the alternative notation output by SVS,

This value, and its standard error, are placed as the last line at the end of the above table of variances.