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sommer (version 1.4)

Solving Mixed Model Equations in R

Description

Mixed model equation solver allowing the specification of variance covariance structures of random effects and residual structures. ML/REML estimates are obtained using the Average Information and/or Expectation-Maximization algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominant and epistatic relationship structures or other covariance structures in R.

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Version

Install

install.packages('sommer')

Monthly Downloads

4,995

Version

1.4

License

GPL-3

Maintainer

Giovanny CovarrubiasPazaran

Last Published

March 24th, 2016

Functions in sommer (1.4)

adiag1

Binds arrays corner-to-corner
PolyData

Genotypic and Phenotypic data for a potato polyploid population
map.plot2

Creating a genetic map
D.mat

Dominance relationship matrix
bathy.colors

Generate a sequence of colors for plotting bathymetric data.
coef.mmer

coef form a GLMM fitted with mmer
anova.mmer

anova form a GLMM fitted with mmer
HDdata

half diallel data for corn hybrids
residuals.mmer

Residuals form a GLMM fitted with mmer
transp

Creating color with transparency
A.mat

Additive relationship matrix
wheatLines

wheat lines dataset
CPdata

Genotypic and Phenotypic data for a CP population (F1; cross between 2 highly heterozygote individuals; i.e. humans, fruit crops, bredding populations in recurrent selection).
AI2

Average Information Algorithm
cornHybrid

Corn crosses and markers
bag

Creating a fixed effect matrix with significant GWAS markers
fdr

False Discovery Rate calculation
big.peaks.col

Peak search by first derivatives
brewer.pal

Generate a sequence of colors for groups.
poe

Short poems from Latin America, and other places why not?
jet.colors

Generate a sequence of colors alog the jet colormap.
AI3

Average Information Algorithm
sommer-package

Solving Mixed Model Equations in R
randef

extracting random effects
Technow_data

Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
E.mat

Epistatic relationship matrix
EMMA

Efficient Mixed Model Association Algorithm
mmer

Mixed Model Equations in R
design.score

design score for the model to be tested
hdm

Half Diallel Matrix
EM2

Expectation Maximization Algorithm
mmer2

Mixed Model Equations in R 2
score.calc

Score calculation for markers
EM

Expectation Maximization Algorithm
fitted.mmer

fitted form a GLMM fitted with mmer
AI

Average Information Algorithm
atcg1234

Letter to number converter
summary.mmer

summary form a GLMM fitted with mmer
plot.mmer

plot form a GLMM plot with mmer