Framework for the analysis of genomic prediction data using R

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Documentation for package ‘synbreed’ version 0.10-5

Help Pages

add.individuals Add new individuals to objects of class gpData
add.markers Add new markers to an object of class gpData
codeGeno Recode genotypic data, imputation of missing values and preselection of markers
create.gpData Create genomic prediction data object
create.pedigree Create pedigree object
cross2gpData Conversion between objects of class 'cross' and 'gpData'
crossVal Cross validation of different prediction models
discard.individuals Subsets for objects of class gpData
discard.markers Subsets for objects of class gpData
gpData2cross Conversion between objects of class 'cross' and 'gpData'
gpData2data.frame Merge of phenotypic and genotypic data
gpMod Genomic predictions models for objects of class gpData
kin Relatedness based on pedigree or marker data
LDDist LD versus distance Plot
LDMap LD Heatmap
manhattanPlot Manhattan plot for SNP effects
MME Mixed Model Equations
pairwiseLD Pairwise LD between markers
plot.GenMap Plot marker map
plot.LDdf Plot function for class 'LDdf'
plot.LDmat Plot function for class 'LDmat'
plot.pedigree Visualization of pedigree
plot.relationshipMatrix Heatmap for relationship Matrix
plotGenMap Plot marker map
plotNeighbourLD Plot neighbour linkage disequilibrium
predict.gpMod Prediction for genomic prediction models.
print.summary.cvData Summary of options and results of the cross validation procedure
print.summary.gpData Summary for class gpData
print.summary.gpMod Summary for class gpMod
print.summary.gpModList Summary for class gpMod
print.summary.pedigree Summary of pedigree information
print.summary.relationshipMatrix Summary of relationship matrices
simul.pedigree Simulation of pedigree structure
simul.phenotype Simulation of a field trial with single trait
summary.cvData Summary of options and results of the cross validation procedure
summary.gpData Summary for class gpData
summary.gpMod Summary for class gpMod
summary.gpModList Summary for class gpMod
summary.LDdf Summary for LD objects
summary.LDmat Summary for LD objects
summary.pedigree Summary of pedigree information
summary.relationshipMatrix Summary of relationship matrices
summaryGenMap Summary of marker map information
write.beagle Prepare genotypic data for Beagle
write.plink Prepare data for PLINK
write.relationshipMatrix Writing relationshipMatrix in table format
[.GenMap Extract or replace part of map data.frame
[.relationshipMatrix Extract or replace part of relationship matrix