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 |