API for polymapR
Linkage Analysis in Outcrossing Polyploids
| Global functions | |
|---|---|
| ALL_dosages | Man page |
| LGHomDf_P1_1 | Man page |
| LGHomDf_P2_1 | Man page |
| LGHomDf_P2_2 | Man page |
| MDSMap_from_list | Man page Source code |
| Mode | Source code |
| P1_DxN_Assigned | Man page |
| P1_SxS_Assigned | Man page |
| P1_homologues | Man page |
| P2_DxN_Assigned | Man page |
| P2_SxS_Assigned | Man page |
| P2_SxS_Assigned_2 | Man page |
| P2_homologues | Man page |
| P2_homologues_triploid | Man page |
| PCA_progeny | Man page Source code |
| SNSN_LOD_deviations | Man page Source code |
| SN_DN_P1 | Man page |
| SN_DN_P2 | Man page |
| SN_SN_P1 | Man page |
| SN_SN_P2 | Man page |
| SN_SN_P2_triploid | Man page |
| SN_SS_P1 | Man page |
| SN_SS_P2 | Man page |
| TRI_dosages | Man page |
| add_dup_markers | Man page Source code |
| all_linkages_list_P1 | Man page |
| all_linkages_list_P1_split | Man page |
| all_linkages_list_P1_subset | Man page |
| assembleDuplexLinks | Man page |
| assign_SN_SN | Man page Source code |
| assign_linkage_group | Man page Source code |
| assign_parental_dosage | Source code |
| bridgeHomologues | Man page Source code |
| calcPotShifts | Source code |
| calcSegtypeInfo | Man page Source code |
| calc_binning_thresholds | Source code |
| calc_q1 | Source code |
| calc_q2 | Source code |
| calc_q3 | Source code |
| calc_qall | Source code |
| checkF1 | Man page Source code |
| checkFilename | Source code |
| check_map | Man page |
| check_marker_assignment | Man page Source code |
| check_maxP | Man page Source code |
| chk1 | Man page |
| chk2integer | Source code |
| cluster_SN_markers | Man page Source code |
| cluster_per_LG | Man page Source code |
| colour.bar | Source code |
| compare_maps | Man page Source code |
| consensus_LG_assignment | Man page Source code |
| consensus_LG_names | Man page Source code |
| convert_marker_dosages | Man page Source code |
| convert_matrix_to_df | Source code |
| convert_polyRAD | Man page Source code |
| convert_updog | Man page Source code |
| correctDosages | Man page Source code |
| createChmHomList | Source code |
| createTetraOriginInput | Man page Source code |
| create_phased_maplist | Man page Source code |
| define_LG_structure | Man page Source code |
| digamfrq | Source code |
| exampleRAD_mapping | Man page |
| finish_linkage_analysis | Man page Source code |
| gcd | Source code |
| gcd_all | Source code |
| getConsensusGeno | Source code |
| getMatchParents | Source code |
| getPargeno | Source code |
| get_markertype_combinations | Man page Source code |
| gp_df | Man page |
| gp_overview | Man page Source code |
| homologue_lg_assignment | Man page Source code |
| integrated.maplist | Man page |
| leftstr | Source code |
| linkage | Man page Source code |
| linkage.gp | Man page Source code |
| linkage.gp.approx | Source code |
| linkage.gp.mappoly | Source code |
| linterpol | Source code |
| makeCombscoresDf | Source code |
| makeProgeny | Source code |
| map1 | Man page |
| map2 | Man page |
| map3 | Man page |
| maplist_P1 | Man page |
| maplist_P1_subset | Man page |
| maplist_P2_subset | Man page |
| marker_assignments_P1 | Man page |
| marker_assignments_P2 | Man page |
| marker_binning | Man page Source code |
| marker_data_summary | Man page Source code |
| merge_homologues | Man page Source code |
| merge_marker_assignments | Source code |
| merge_marker_assignments.gp | Source code |
| mout | Man page |
| overviewSNlinks | Man page Source code |
| p4_1.0_1.0 | Source code |
| p4_1.0_1.1 | Source code |
| p4_1.0_1.2 | Source code |
| p4_1.0_1.3 | Source code |
| p4_1.0_2.0 | Source code |
| p4_1.0_2.1 | Source code |
| p4_1.0_2.2 | Source code |
| p4_1.1_1.1 | Source code |
| p4_1.1_1.2 | Source code |
| p4_1.1_1.3 | Source code |
| p4_1.1_2.2 | Source code |
| p4_1.2_1.2 | Source code |
| p4_1.2_2.1 | Source code |
| p4_1.2_2.2 | Source code |
| p4_1.3_1.2 | Source code |
| p4_1.3_1.3 | Source code |
| p4_1.3_2.1 | Source code |
| p4_1.3_2.2 | Source code |
| p4_2.0_1.1 | Source code |
| p4_2.0_1.2 | Source code |
| p4_2.0_1.3 | Source code |
| p4_2.0_2.0 | Source code |
| p4_2.0_2.1 | Source code |
| p4_2.0_2.2 | Source code |
| p4_2.1_2.2 | Source code |
| p4_2.2_2.2 | Source code |
| p4_functions | Man page |
| p6_1.0_1.0 | Source code |
| parental_quantities | Man page Source code |
| phase_SN_diploid | Man page Source code |
| phased.maplist | Man page |
| plot_SNlinks | Source code |
| plot_hom_vs_LG | Man page Source code |
| plot_linkage_df | Man page Source code |
| plot_map | Man page Source code |
| plot_phased_maplist | Man page Source code |
| polygamfrq | Source code |
| polymapR | Man page |
| polymapR-package | Man page |
| prepare_pwd | Source code |
| r2_1.0_1.0 | Man page Source code |
| r2_1.0_1.1 | Man page Source code |
| r2_1.1_1.1 | Man page Source code |
| r2_functions | Man page |
| r3_0.1_0.1 | Man page Source code |
| r3_0.1_1.1 | Man page Source code |
| r3_0.1_2.1 | Man page Source code |
| r3_1.0_1.0 | Source code |
| r3_1.0_1.1 | Source code |
| r3_1.0_2.0 | Source code |
| r3_1.0_2.1 | Source code |
| r3_1.1_1.1 | Source code |
| r3_1.1_2.1 | Source code |
| r3_2.0_1.1 | Source code |
| r3_2.0_2.0 | Source code |
| r3_2.0_2.1 | Source code |
| r3_2.1_2.1 | Man page Source code |
| r3_functions | Man page |
| r4_1.0_1.0 | Source code |
| r4_1.0_1.1 | Source code |
| r4_1.0_1.2 | Source code |
| r4_1.0_1.3 | Source code |
| r4_1.0_2.0 | Source code |
| r4_1.0_2.1 | Source code |
| r4_1.0_2.2 | Source code |
| r4_1.1_1.1 | Source code |
| r4_1.1_1.2 | Source code |
| r4_1.1_1.3 | Source code |
| r4_1.1_2.2 | Source code |
| r4_1.2_1.2 | Source code |
| r4_1.2_2.1 | Source code |
| r4_1.2_2.2 | Source code |
| r4_1.3_1.2 | Source code |
| r4_1.3_1.3 | Source code |
| r4_1.3_2.1 | Source code |
| r4_1.3_2.2 | Source code |
| r4_2.0_1.1 | Source code |
| r4_2.0_1.2 | Source code |
| r4_2.0_1.3 | Source code |
| r4_2.0_2.0 | Source code |
| r4_2.0_2.1 | Source code |
| r4_2.0_2.2 | Source code |
| r4_2.1_2.1 | Source code |
| r4_2.1_2.2 | Source code |
| r4_2.2_2.2 | Source code |
| r4_functions | Man page |
| r6_1.0_1.0 | Source code |
| r6_1.0_1.1 | Source code |
| r6_1.0_1.2 | Source code |
| r6_1.0_1.3 | Source code |
| r6_1.0_1.4 | Source code |
| r6_1.0_1.5 | Source code |
| r6_1.0_2.0 | Source code |
| r6_1.0_2.1 | Source code |
| r6_1.0_2.2 | Source code |
| r6_1.0_2.3 | Source code |
| r6_1.0_2.4 | Source code |
| r6_1.0_3.0 | Source code |
| r6_1.0_3.1 | Source code |
| r6_1.0_3.2 | Source code |
| r6_1.0_3.3 | Source code |
| r6_1.0_4.1 | Source code |
| r6_1.1_1.1 | Source code |
| r6_1.1_1.2 | Source code |
| r6_1.1_1.3 | Source code |
| r6_1.1_1.4 | Source code |
| r6_1.1_1.5 | Source code |
| r6_1.1_2.0 | Source code |
| r6_1.1_2.2 | Source code |
| r6_1.1_2.3 | Source code |
| r6_1.1_2.4 | Source code |
| r6_1.1_3.0 | Source code |
| r6_1.1_3.3 | Source code |
| r6_1.2_1.2 | Source code |
| r6_1.2_1.3 | Source code |
| r6_1.2_1.4 | Source code |
| r6_1.2_1.5 | Source code |
| r6_1.2_2.1 | Source code |
| r6_1.2_2.2 | Source code |
| r6_1.2_2.3 | Source code |
| r6_1.2_2.4 | Source code |
| r6_1.2_3.0 | Source code |
| r6_1.2_3.1 | Source code |
| r6_1.2_3.2 | Source code |
| r6_1.2_3.3 | Source code |
| r6_1.2_4.1 | Source code |
| r6_1.3_1.3 | Source code |
| r6_1.3_1.4 | Source code |
| r6_1.3_1.5 | Source code |
| r6_1.3_2.2 | Source code |
| r6_1.3_2.3 | Source code |
| r6_1.3_2.4 | Source code |
| r6_1.3_3.1 | Source code |
| r6_1.3_3.2 | Source code |
| r6_1.3_3.3 | Source code |
| r6_1.3_4.1 | Source code |
| r6_1.4_1.4 | Source code |
| r6_1.4_1.5 | Source code |
| r6_1.4_2.2 | Source code |
| r6_1.4_2.3 | Source code |
| r6_1.4_2.4 | Source code |
| r6_1.4_3.2 | Source code |
| r6_1.4_3.3 | Source code |
| r6_1.4_4.1 | Source code |
| r6_1.5_1.5 | Source code |
| r6_1.5_2.2 | Source code |
| r6_1.5_2.3 | Source code |
| r6_1.5_2.4 | Source code |
| r6_1.5_3.2 | Source code |
| r6_1.5_3.3 | Source code |
| r6_2.0_1.2 | Source code |
| r6_2.0_1.3 | Source code |
| r6_2.0_1.4 | Source code |
| r6_2.0_1.5 | Source code |
| r6_2.0_2.0 | Source code |
| r6_2.0_2.1 | Source code |
| r6_2.0_2.2 | Source code |
| r6_2.0_2.3 | Source code |
| r6_2.0_2.4 | Source code |
| r6_2.0_3.0 | Source code |
| r6_2.0_3.1 | Source code |
| r6_2.0_3.2 | Source code |
| r6_2.0_3.3 | Source code |
| r6_2.0_4.1 | Source code |
| r6_2.1_1.5 | Source code |
| r6_2.1_2.4 | Source code |
| r6_2.1_3.0 | Source code |
| r6_2.2_2.2 | Source code |
| r6_2.2_2.3 | Source code |
| r6_2.2_2.4 | Source code |
| r6_2.2_3.2 | Source code |
| r6_2.2_3.3 | Source code |
| r6_2.3_2.3 | Source code |
| r6_2.3_2.4 | Source code |
| r6_2.3_3.2 | Source code |
| r6_2.3_3.3 | Source code |
| r6_2.4_2.4 | Source code |
| r6_3.0_1.3 | Source code |
| r6_3.0_1.4 | Source code |
| r6_3.0_1.5 | Source code |
| r6_3.0_2.2 | Source code |
| r6_3.0_2.3 | Source code |
| r6_3.0_2.4 | Source code |
| r6_3.0_3.0 | Source code |
| r6_3.0_3.1 | Source code |
| r6_3.0_3.2 | Source code |
| r6_3.0_3.3 | Source code |
| r6_3.0_4.1 | Source code |
| r6_3.3_2.4 | Source code |
| r6_3.3_3.3 | Source code |
| r6_functions | Man page |
| r_LOD_plot | Man page Source code |
| rightstr | Source code |
| screen_for_NA_values | Man page Source code |
| screen_for_duplicate_individuals | Man page Source code |
| screen_for_duplicate_individuals.gp | Man page Source code |
| screen_for_duplicate_markers | Man page Source code |
| screened_data | Man page |
| screened_data2 | Man page |
| screened_data3 | Man page |
| segregating_data | Man page |
| segtypeInfoSummary | Source code |
| selSegtypeInfo | Source code |
| test_LG_hom_stack | Source code |
| test_cluster_stack | Source code |
| test_dosage_matrix | Source code |
| test_linkage_df | Source code |
| test_prefpairing | Man page Source code |
| test_probgeno_df | Source code |
| vector.to.matrix | Source code |
| write.TSNPM | Man page Source code |
| write.logheader | Source code |
| write.mct | Man page Source code |
| write.pwd | Man page Source code |
| write_nested_list | Man page Source code |
| write_pwd_list | Man page Source code |
