| add_dup_markers | Add duplicate markers to a map |
| ALL_dosages | A dosage matrix for a random pairing tetraploid with five... |
| all_linkages_list_P1 | A (nested) list of linkage data frames classified per linkage... |
| assign_linkage_group | Assign non-SN markers to a linkage group and homologue(s). |
| assign_SN_SN | Assign (leftover) 1.0 markers |
| bridgeHomologues | Use bridge markers to cluster homologues into linkage groups |
| calc_binning_thresholds | calc_binning_thresholds |
| calcPotShifts | Calculate potential shifts in marker dosages |
| calc_q1 | calc_q1... |
| calc_q2 | calc_q2... |
| calc_q3 | calc_q3... |
| calc_qall | calc_qall... |
| calcSegtypeInfo | Build a list of segregation types |
| checkF1 | Identify the best-fitting F1 segregation types |
| checkFilename | checkFilename... |
| check_map | Check the quality of a linkage map using heatplots |
| check_marker_assignment | Check for consistent marker assignment between both parents |
| chk2integer | chk2integer... |
| cluster_per_LG | Cluster 1.0 markers into correct homologues per linkage group |
| cluster_SN_markers | Cluster 1.0 markers |
| colour.bar | Add colour bar scale to heatplot |
| consensus_LG_assignment | Consensus LG assignment |
| consensus_LG_names | Find consensus linkage group names |
| convert_marker_dosages | Convert marker dosages to the basic types. |
| correctDosages | Check if dosage scores may have to be shifted |
| createChmHomList | User interface for specifying linkage group for a homologue |
| createMap | Marker ordering function |
| create_phased_maplist | Create a phased homologue map list using the original dosages |
| createTetraOriginInput | Create input files for TetraOrigin using an integrated... |
| define_LG_structure | Generate linkage group and homologue structure of SxN markers |
| digamfrq | digamfrq... |
| finish_linkage_analysis | Linkage analysis between all markertypes within LG. |
| gcd | gcd... |
| gcd_all | gcd_all... |
| getConsensusGeno | getConsensusGeno... |
| get_markertype_combinations | Visualize and get all markertype combinations for which there... |
| getMatchParents | getMatchParents... |
| homologue_lg_assignment | Assign markers to linkage groups and homologues. |
| integrated.maplist | A nested list with integrated maps |
| leftstr | Get substrings from the lefthand side |
| LGHomDf_P1_1 | A 'data.frame' specifying the assigned homologue and linkage... |
| linkage | Calculate recombination frequency, LOD and phase |
| linterpol | linterpol... |
| makeProgeny | makeProgeny... |
| maplist_P1 | A list of maps of one parent |
| marker_binning | Perform binning of markers. |
| marker_binning_list | Bin markers that are in a nested list |
| marker_data_summary | Summarize marker data |
| MDSMap_from_list | Wrapper function for MDSMap to generate linkage maps from... |
| merge_homologues | Merge homologues |
| merge_marker_assignments | Merge marker assignments |
| Mode | Calculate the mode of a vector |
| orient_and_merge_maps | Align and integrate maps |
| overviewSNlinks | Plotting 1.0 links between homologues |
| P1_homologues | A list of cluster stacks at different LOD scores |
| P1_SxS_Assigned | A 'data.frame' with marker assignments |
| p4_functions | Calculate recombination frequency, LOD and log-likelihood... |
| parental_quantities | Calculate frequency of each markertype. |
| PCA_progeny | Perform a PCA on progeny |
| phased.maplist | A list of phased maps |
| phase_SN_diploid | Phase 1.0 markers at the diploid level |
| plot_hom_vs_LG | Plot homologue position versus integrated positions |
| plot_linkage_df | Plot r versus LOD grouped by phase |
| plot_map | Plot linkage maps |
| plot_phased_maplist | Visualise the phased homologue maplist |
| plot_SNlinks | Plot links between 1.0 markers |
| polygamfrq | polygamfrq... |
| polymapR | Linkage analysis in polyploids |
| prepare_pwd | Prepare pwd for mapping scripts e.g. MDSmap |
| r3_functions | Calculate recombination frequency, LOD and log-likelihood... |
| r4_functions | Calculate recombination frequency, LOD and log-likelihood... |
| r6_functions | Calculate recombination frequency, LOD and log-likelihood... |
| rightstr | Get substrings from the righthand side |
| r_LOD_plot | Plot r versus LOD |
| screen_for_duplicate_individuals | Screen for duplicate individuals |
| screen_for_duplicate_markers | Screen for and remove duplicated markers |
| screen_for_NA_values | Screen marker data for NA values |
| segtypeInfoSummary | Summarize the segtypeInfo list |
| selSegtypeInfo | Restrict a list of segregation types to specified inheritance... |
| SNSN_LOD_deviations | Identify deviations in LOD scores between pairs of simplex x... |
| SN_SN_P1 | A linkage 'data.frame'. |
| split_linkage_info | Split linkage information into homologues |
| test_cluster_stack | Error and warning handling for cluster_stack |
| test_dosage_matrix | Error and warning handling for dosage_matrix |
| test_LG_hom_stack | Error and warning handling for LG_hom_stack |
| test_linkage_df | Error and warning handling for linkage_df |
| test_prefpairing | Check for and estimate preferential pairing |
| vector.to.matrix | Large vector or in standardized matrix |
| write.logheader | Write a header for the log file |
| write.mct | Write MapChart file |
| write_nested_list | Write out a nested list |
| write.pwd | Write a JoinMap compatible .pwd file from linkage data.frame. |
| write_pwd_list | Write pwd files from a nested list |
