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Small pedigree based mixed model example

April 8, 2012

Pedigree based mixed models (often called animal models, due to modelling animal performance) are the cornerstone of animal breeding and quantitative genetics. There are many programs that can be used for analyzing your data with these models, e.g., ASREML, BLUPf90, MATVEC, MiXBLUP & MiX99, SurvivalKit, PEST/VCE, WOMBAT, ...). There are also R packages you...

Regression – covariate adjustment

April 3, 2012

By Gregor Gorjanc

Linear regression is one of the key concepts in statistics . However, people are often confuse the meaning of parameters of linear regression - the intercept tells us the average value of y at x=0, while the slope tells us how m...

GBLUP example in R

March 30, 2012

By Gregor Gorjanc

Shirin Amiri was asking about GBLUP (genomic BLUP) and based on her example I set up the following R script to show how GBLUP works. Note that this is the so called marker model, where we estimate allele substitution effects of the markers and not individual based model, where genomic breeding values are inferred directly. The code:

library(package="MatrixModels")
 
dat <- data.frame(...
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Polyploidy in sugarcane

September 28, 2011

By Gregor Gorjanc

While reading UseR conference abstracts I came across this sentence: "Sugarcane is polypoid, i.e., has 8 to 14 copies of every chromosome, with individual alleles in varying numbers." Vau! This generates really complex genotype system. Say we have biallelic gene with alleles being A and B. In diploids the possible genotypes are AA, AB, and BB. Given the...

Setup up the inverse of additive relationship matrix in R

August 11, 2011

By Gregor Gorjanc

Setup up the inverse of additive relationship matrix in R

Additive genetic covariance between individuals is one of the key concepts in (quantitative) genetics. When doing the prediction of additive genetic values for pedigree members, we need the inverse of the so called numerator relationship matr...

gRain: genetics example

April 14, 2011

By Gregor Gorjanc

gRain is an R package for "probability propagation in graphical independence networks, also known as probabilistic expert systems (which includes Bayesian networks as a special case)". This package caught my attention because some genetic models can b...