| ASRgenomics-package | ASRgenomics: Complementary Genomic Functions |
| callrate | Estimates call rate |
| check.args_ | Check string arguments |
| check.data_ | Check data class |
| check.data.mode_ | Check data mode |
| check.logical_ | Check logical arguments |
| dummy.map_ | Creates a dummy map if not provided |
| Fis | Estimates the population level inbreeding (Fis) by marker |
| full2sparse | Generates a sparse form matrix from a full form matrix |
| 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 |
| G.inverse | Obtains the inverse of the genomic relationship matrix G |
| G.matrix | Obtains the genomic matrix from SNP data for additive or... |
| G.predict | Generates the conditional predictions of random effects... |
| G.tuneup | Tune-up the the genomic relationship matrix G |
| heterozygosity | Estimates observed and expected heterozygosity |
| 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... |
| kinship.heatmap | Enhanced heatmap plot for a kinship matrix K |
| kinship.pca | Performs a Principal Component Analysis (PCA) based on a... |
| Kinv.condition | Assess condition of the inverse of *K* |
| maf | Estimates minor allele frequency (MAF) |
| match.G2A | Check the genomic relationship matrix G against the pedigree... |
| 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... |
| silent_ | Function that silences everything (e.g., 'cat()', 'print()',... |
| snp.pca | Performs a Principal Component Analysis (PCA) based on a... |
| snp.pruning | Reduces the number of redundant markers on a molecular matrix... |
| 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... |
