# Framework for the Analysis of Genomic Prediction Data using R

## Documentation for package ‘synbreed’ version 0.12-9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

add.gpData | Join two 'gpData' objects
add.individuals | Add new individuals to objects of class gpData
add.markers | Add new markers to an object of class gpData
add.pedigree | Merge 'pedigree' object
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
read.vcf2list | Read data of a vcf-file to a matrix
read.vcf2matrix | Read data of a vcf-file to a matrix
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
write.vcf | Prepare genotypic data in vcf-Format
[.GenMap | Extract or replace part of map data.frame
[.relationshipMatrix | Extract or replace part of relationship matrix