Linkage Analysis in Outcrossing Polyploids
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Documentation for package ‘polymapR’ version 1.1.5
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A B C D E F G H I L M O P R S T W
-- A --
| add_dup_markers | Add back duplicate markers after mapping |
| ALL_dosages | A dosage matrix for a random pairing tetraploid with five linkage groups. |
| all_linkages_list_P1 | A (nested) list of linkage data frames classified per linkage group and homologue |
| all_linkages_list_P1_split | A (nested) list of linkage data frames classified per linkage group and homologue |
| all_linkages_list_P1_subset | A (nested) list of linkage data frames classified per linkage group and homologue |
| assembleDuplexLinks | Use bridge markers to cluster homologues into linkage groups |
| assign_linkage_group | Assign non-SN markers to a linkage group and homologue(s). |
| assign_SN_SN | Assign (leftover) 1.0 markers |
-- B --
| bridgeHomologues | Use bridge markers to cluster homologues into linkage groups |
-- C --
| calcSegtypeInfo | Build a list of segregation types |
| checkF1 | Identify the best-fitting F1 segregation types |
| check_map | Check the quality of a linkage map using heatplots |
| check_marker_assignment | Check for consistent marker assignment between both parents |
| check_maxP | check your dataset's maxP distribution |
| chk1 | Example output of the checkF1 function |
| cluster_per_LG | Cluster 1.0 markers into correct homologues per linkage group |
| cluster_SN_markers | Cluster 1.0 markers |
| compare_maps | Compare linkage maps, showing links between connecting markers common to neighbouring maps |
| consensus_LG_assignment | Consensus LG assignment |
| consensus_LG_names | Find consensus linkage group names |
| convert_marker_dosages | Convert marker dosages to the basic types. |
| convert_polyRAD | Convert (probabilistic) genotype calling results from polyRAD to input compatible with polymapR |
| convert_updog | Convert (probabilistic) genotype calling results from updog to input compatible with polymapR. |
| correctDosages | Check if dosage scores may have to be shifted |
| createTetraOriginInput | Create input files for TetraOrigin using an integrated linkage map list and marker dosage matrix |
| create_phased_maplist | Create a phased homologue map list using the original dosages |
-- D --
| define_LG_structure | Generate linkage group and homologue structure of SxN markers |
-- E --
| exampleRAD_mapping | Example output dataset of polyRAD::PipelineMapping2Parents function |
-- F --
| finish_linkage_analysis | Linkage analysis between all markertypes within a linkage group. |
-- G --
| get_markertype_combinations | Visualize and get all markertype combinations for which there are functions in polymapR |
| gp_df | An example of a genotype probability data frame |
| gp_overview | gp_overview |
| gp_vignette_data | A list of objects needed to build the probabilistic genotype vignette |
-- H --
| homologue_lg_assignment | Assign markers to linkage groups and homologues. |
-- I --
| integrated.maplist | A nested list with integrated maps |
-- L --
| LGHomDf_P1_1 | A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker |
| LGHomDf_P2_1 | A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker |
| LGHomDf_P2_2 | A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker |
| linkage | Calculate recombination frequency, LOD and phase |
| linkage.gp | Calculate recombination frequency, LOD and phase using genotype probabilities |
-- M --
| map1 | A sample map |
| map2 | A sample map |
| map3 | A sample map |
| maplist_P1 | A list of maps of one parent |
| maplist_P1_subset | A list of maps of one parent |
| maplist_P2_subset | A list of maps of one parent |
| marker_assignments_P1 | A 'data.frame' with marker assignments |
| marker_assignments_P2 | A 'data.frame' with marker assignments |
| marker_binning | Perform binning of markers. |
| marker_data_summary | Summarize marker data |
| MDSMap_from_list | Wrapper function for MDSMap to generate linkage maps from list of pairwise linkage estimates |
| merge_homologues | Merge homologues |
| mout | Example output dataset of updog::multidog function |
-- O --
| overviewSNlinks | Plotting 1.0 links between homologues |
-- P --
| P1_DxN_Assigned | A 'data.frame' with marker assignments |
| P1_homologues | A list of cluster stacks at different LOD scores |
| P1_SxS_Assigned | A 'data.frame' with marker assignments |
| P2_DxN_Assigned | A 'data.frame' with marker assignments |
| P2_homologues | A list of cluster stacks at different LOD scores |
| P2_homologues_triploid | A list of cluster stacks at different LOD scores |
| P2_SxS_Assigned | A 'data.frame' with marker assignments |
| P2_SxS_Assigned_2 | A 'data.frame' with marker assignments |
| p4_functions | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid |
| 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_map | Plot linkage maps |
| plot_phased_maplist | Visualise the phased homologue maplist |
-- R --
| r2_1.0_1.0 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross. |
| r2_1.0_1.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross. |
| r2_1.1_1.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross. |
| r2_functions | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross. |
| r3_2_1.0_1.0 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross. |
| r3_2_1.0_1.1 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross. |
| r3_2_1.0_1.2 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross. |
| r3_2_1.2_1.2 | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross. |
| r3_functions | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross. |
| r4_functions | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid |
| r6_functions | Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid |
| r_LOD_plot | Plot r versus LOD |
-- S --
| screened_data | A dosage matrix for a random pairing tetraploid with five linkage groups. |
| screened_data2 | A dosage matrix for a random pairing tetraploid with five linkage groups. |
| screened_data3 | A dosage matrix for a random pairing tetraploid with five linkage groups. |
| screen_for_duplicate_individuals | Screen for duplicate individuals |
| screen_for_duplicate_individuals.gp | Screen for duplicate individuals using weighted genotype probabilities |
| screen_for_duplicate_markers | Screen for and remove duplicated markers |
| screen_for_NA_values | Screen marker data for NA values |
| segregating_data | A dosage matrix for a random pairing tetraploid with five linkage groups. |
| SNSN_LOD_deviations | Identify deviations in LOD scores between pairs of simplex x nulliplex markers |
| SN_DN_P1 | A linkage 'data.frame'. |
| SN_DN_P2 | A linkage 'data.frame'. |
| SN_SN_P1 | A linkage 'data.frame'. |
| SN_SN_P2 | A linkage 'data.frame'. |
| SN_SN_P2_triploid | A linkage 'data.frame'. |
| SN_SS_P1 | A linkage 'data.frame'. |
| SN_SS_P2 | A linkage 'data.frame'. |
-- T --
| test_prefpairing | Check for and estimate preferential pairing |
| TRI_dosages | A dosage matrix for a random pairing tetraploid with five linkage groups. |
-- W --
| write.mct | Write MapChart file |
| write.pwd | Write a JoinMap compatible .pwd file from linkage data.frame. |
| write.TSNPM | Write TetraploidSNPMap input file |
| write_nested_list | Write out a nested list |
| write_pwd_list | Write pwd files from a nested list |