| BLUE | Calculate Best Linear Unbiased Estimates using linear mixed... |
| BLUEs.pheno | A data-frame of best linear unbiased predicted (BLUE)... |
| bx | Rcpp internal function Backward from forward-backward... |
| check_cofactors | Build a multi-QTL model using step-wise procedure of checking... |
| convert_mappoly_to_phased.maplist | Function to extract the phased map from a mappoly.map object |
| count_recombinations | Predict recombination breakpoints using IBD probabilities |
| estimate_GIC | Estimate the Genotypic Information Coefficient (GIC) |
| estimate_IBD | Generate IBD probabilities from marker genotypes and a phased... |
| exploreQTL | Explore the possible segregation type of a QTL peak using... |
| findPeak | Function to find the position of maximum LOD on a particular... |
| findSupport | Function to find a LOD - x support interval around a QTL... |
| fx | Rcpp internal function Forward from forward-backward... |
| GIC_4x | A list of GIC estimates (4x) |
| hexa.list | A list of hexaploid bivalent pairing configurations |
| IBD_4x | A list of identity-by-descent probabilities (4x) |
| import_IBD | Import IBD probabilities as estimated by TetraOrigin |
| impute_dosages | Re-estimate marker dosages given IBD input estimated using a... |
| maxL_IBD | Wrapper function to run estimate_IBD function over multiple... |
| meiosis_report | Generate a 'report' of predicted meiotic behaviour in an F1... |
| mr.ls | A list of pairing predictions (4x) |
| phased_maplist.4x | A list of phased maps (4x) |
| Phenotypes_4x | A data-frame of phenotypes (4x) |
| plotLinearQTL | Plot the results of genome-wide QTL analysis along a single... |
| plotLinearQTL_list | Overlay the results of a number of genome-wide QTL analysis... |
| plotQTL | Plot the results of a previous QTL analysis |
| plotRecLS | Plot the recombination landscape across the genome |
| polyqtlR | QTL analysis in polyploid species using identity-by-descent... |
| PVE | Function to determine the percentage variance explained (PVE)... |
| qtl_LODs.4x | A list of QTL results (4x) |
| QTLscan | General QTL function that allows for co-factors, completely... |
| Rec_Data_4x | A list of recombination count data (4x) |
| rem.hex | Redundant genotype classes in hexavalent transition matrix... |
| rem.quad | Redundant genotype classes in quadrivalent transition matrix... |
| segList_2x | A list of all possible bi-allelic QTL segregation types (2x) |
| segList_3x | A list of all possible bi-allelic QTL segregation types (3x) |
| segList_4x | A list of all possible bi-allelic QTL segregation types (4x) |
| segList_6x | A list of all possible bi-allelic QTL segregation types (6x) |
| segMaker | Create a list of possible QTL segregation types |
| singleMarkerRegression | Run a single marker regression using marker dosages |
| SNP_dosages.4x | A matrix of SNP marker dosages (4x) |
| spline_IBD | Fit splines to IBD probabilities |
| thinmap | Thin out map data |
| visualiseGIC | Visualise Genotypic Information Coefficient |
| visualiseHaplo | Visualise haplotypes in certain individuals in a certain... |
| visualisePairing | Visualise pairing of parental homologues |
| visualiseQTLeffects | Visualise QTL homologue effects around a QTL position |
