LDDist                  LD versus distance Plot
LDMap                   LD Heatmap
MME                     Mixed Model Equations
[.GenMap                Extract or replace part of map data.frame
[.relationshipMatrix    Extract or replace part of relationship matrix
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
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
manhattanPlot           Manhattan plot for SNP effects
pairwiseLD              Pairwise LD between markers
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.
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.LDdf            Summary for LD objects
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.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
