full2sparse |
Generates a sparse form matrix from a full form matrix |

G.inverse |
Obtains the inverse of the genomic relationship matrix G |

G.matrix |
Obtains the genomic matrix from SNP data for additive or dominant relationships |

G.predict |
Generates the conditional predictions of random effects (BLUPs) |

G.tuneup |
Tune-up the the genomic relationship matrix G |

geno.apple |
Genotypic data for apple dataset |

geno.pine655 |
Genotypic data of 655 genotypes for loblolly pine dataset |

geno.pine926 |
Genotypic data of 926 genotypes for loblolly pine dataset |

geno.salmon |
Genotypic data for Atlantic salmon dataset |

H.inverse |
Generates the inverse of the hybrid H matrix |

H.matrix |
Generates the hybrid H matrix |

kinship.diagnostics |
Reports summary statistics, plots and filter options for a given kinship matrix K |

kinship.heatmap |
Enhanced heatmap plot for a kinship matrix K |

kinship.pca |
Performs a Principal Component Analysis (PCA) based on a kinship matrix K |

match.G2A |
Check the genomic relationship matrix G against the pedigree relationship matrix A or vice versa |

match.kinship2pheno |
Check any kinship matrix K against phenotypic data |

ped.pine |
Pedigree data for loblolly pine dataset |

ped.salmon |
Pedigree data for Atlantic salmon dataset |

pheno.apple |
Phenotypic data for apple dataset |

pheno.pine |
Phenotypic data for loblolly pine dataset |

pheno.salmon |
Phenotypic data for Atlantic salmon dataset |

qc.filtering |
Quality control filtering of molecular matrix M for downstream analyses |

snp.pca |
Performs a Principal Component Analysis (PCA) based on a molecular matrix M |

snp.pruning |
Reduces the number of redundant markers on a molecular matrix M by pruning |

snp.recode |
Recodes the molecular matrix M for downstream analyses |

sparse2full |
Generates a full matrix form from a sparse form matrix |

synthetic.cross |
Generates a molecular matrix M for hypothetical crosses based on the genomic information of the parents |