Man pages for synbreed
Framework for the Analysis of Genomic Prediction Data using R
| 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 |
| cattle | Dairy cattle data |
| codeGeno | Recode genotypic data, imputate missing values and preselect... |
| 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 |
| Extract.GenMap | Extract or replace part of map data.frame |
| Extract.relationshipMatrix | Extract or replace part of relationship matrix |
| 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 |
| kinship | Relatedness based on pedigree or marker data |
| LD | Pairwise LD between markers |
| LDDist | LD versus distance Plot |
| LDMap | LD Heatmap |
| maize | Simulated maize data |
| manhattanPlot | Manhattan plot for SNP effects |
| mice | Heterogenous stock mice population |
| MME | Mixed Model Equations |
| plot.genMap | Plot marker map |
| plot.LDdf | Plot function for class 'LDdf' |
| plot.LDmat | Plot function for class 'LDmat' |
| plotNeighbourLD | Plot neighbour linkage disequilibrium |
| plot.pedigree | Visualization of pedigree |
| plot.relationshipMatrix | Heatmap for relationship Matrix |
| 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.cvData | Summary of options and results of the cross validation... |
| summary.gpData | Summary for class gpData |
| summary.gpMod | Summary for class gpMod |
| summary.LDdf | Summary for LD objects |
| summary.map | Summary of marker map information |
| summary.pedigree | Summary of pedigree information |
| summary.relationshipMatrix | Summary of relationship matrices |
| 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 |
