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"check_marker_assignment" ] }, { "page": "check_maxP", "title": "check your dataset's maxP distribution", "topics": [ "check_maxP" ] }, { "page": "checkF1", "title": "Identify the best-fitting F1 segregation types", "topics": [ "checkF1" ] }, { "page": "chk1", "title": "Example output of the checkF1 function", "topics": [ "chk1" ] }, { "page": "cluster_per_LG", "title": "Cluster 1.0 markers into correct homologues per linkage group", "topics": [ "cluster_per_LG" ] }, { "page": "cluster_SN_markers", "title": "Cluster 1.0 markers", "topics": [ "cluster_SN_markers" ] }, { "page": "compare_maps", "title": "Compare linkage maps, showing links between connecting markers common to neighbouring maps", "topics": [ "compare_maps" ] }, { "page": "consensus_LG_assignment", "title": "Consensus LG assignment", "topics": [ "consensus_LG_assignment" ] }, { "page": "consensus_LG_names", "title": "Find consensus linkage group names", "topics": [ "consensus_LG_names" ] }, { "page": "convert_marker_dosages", "title": "Convert marker dosages to the basic types.", "topics": [ "convert_marker_dosages" ] }, { "page": "convert_polyRAD", "title": "Convert (probabilistic) genotype calling results from polyRAD to input compatible with polymapR", "topics": [ "convert_polyRAD" ] }, { "page": "convert_updog", "title": "Convert (probabilistic) genotype calling results from updog to input compatible with polymapR.", "topics": [ "convert_updog" ] }, { "page": "correctDosages", "title": "Check if dosage scores may have to be shifted", "topics": [ "correctDosages" ] }, { "page": "create_phased_maplist", "title": "Create a phased homologue map list using the original dosages", "topics": [ "create_phased_maplist" ] }, { "page": "createTetraOriginInput", "title": "Create input files for TetraOrigin using an integrated linkage map list and marker dosage matrix", "topics": [ "createTetraOriginInput" ] }, { "page": "define_LG_structure", "title": "Generate linkage group and homologue structure of SxN markers", "topics": [ "define_LG_structure" ] }, { "page": "exampleRAD_mapping", "title": "Example output dataset of polyRAD::PipelineMapping2Parents function", "topics": [ "exampleRAD_mapping" ] }, { "page": "finish_linkage_analysis", "title": "Linkage analysis between all markertypes within a linkage group.", "topics": [ "finish_linkage_analysis" ] }, { "page": "get_markertype_combinations", "title": "Visualize and get all markertype combinations for which there are functions in polymapR", "topics": [ "get_markertype_combinations" ] }, { "page": "gp_df", "title": "An example of a genotype probability data frame", "topics": [ "gp_df" ] }, { "page": "gp_overview", "title": "gp_overview", "topics": [ "gp_overview" ] }, { "page": "gp_vignette_data", "title": "A list of objects needed to build the probabilistic genotype vignette", "topics": [ "gp_vignette_data" ] }, { "page": "homologue_lg_assignment", "title": "Assign markers to linkage groups and homologues.", "topics": [ "homologue_lg_assignment" ] }, { "page": "integrated.maplist", "title": "A nested list with integrated maps", "topics": [ "integrated.maplist" ] }, { "page": "LGHomDf_P1_1", "title": "A 'data.frame' specifying the assigned homologue and linkage group number per SxN marker", "topics": [ "LGHomDf_P1_1", "LGHomDf_P2_1", "LGHomDf_P2_2" ] }, { "page": "linkage", "title": "Calculate recombination frequency, LOD and phase", "topics": [ "linkage" ] }, { "page": "linkage.gp", "title": "Calculate recombination frequency, LOD and phase using genotype probabilities", "topics": [ "linkage.gp" ] }, { "page": "map1", "title": "A sample map", "topics": [ "map1" ] }, { "page": "map2", "title": "A sample map", "topics": [ "map2" ] }, { "page": "map3", "title": "A sample map", "topics": [ "map3" ] }, { "page": "maplist_P1", "title": "A list of maps of one parent", "topics": [ "maplist_P1", "maplist_P1_subset", "maplist_P2_subset" ] }, { "page": "marker_binning", "title": "Perform binning of markers.", "topics": [ "marker_binning" ] }, { "page": "marker_data_summary", "title": "Summarize marker data", "topics": [ "marker_data_summary" ] }, { "page": "MDSMap_from_list", "title": "Wrapper function for MDSMap to generate linkage maps from list of pairwise linkage estimates", "topics": [ "MDSMap_from_list" ] }, { "page": "merge_homologues", "title": "Merge homologues", "topics": [ "merge_homologues" ] }, { "page": "mout", "title": "Example output dataset of updog::multidog function", "topics": [ "mout" ] }, { "page": "overviewSNlinks", "title": "Plotting 1.0 links between homologues", "topics": [ "overviewSNlinks" ] }, { "page": "P1_homologues", "title": "A list of cluster stacks at different LOD scores", "topics": [ "P1_homologues", "P2_homologues", "P2_homologues_triploid" ] }, { "page": "P1_SxS_Assigned", "title": "A 'data.frame' with marker assignments", "topics": [ "marker_assignments_P1", "marker_assignments_P2", "P1_DxN_Assigned", "P1_SxS_Assigned", "P2_DxN_Assigned", "P2_SxS_Assigned", "P2_SxS_Assigned_2" ] }, { "page": "p4_functions", "title": "Calculate recombination frequency, LOD and log-likelihood from frequency tables in a preferential pairing tetraploid", "topics": [ "p4_functions" ] }, { "page": "parental_quantities", "title": "Calculate frequency of each markertype.", "topics": [ "parental_quantities" ] }, { "page": "PCA_progeny", "title": "Perform a PCA on progeny", "topics": [ "PCA_progeny" ] }, { "page": "phase_SN_diploid", "title": "Phase 1.0 markers at the diploid level", "topics": [ "phase_SN_diploid" ] }, { "page": "phased.maplist", "title": "A list of phased maps", "topics": [ "phased.maplist" ] }, { "page": "plot_hom_vs_LG", "title": "Plot homologue position versus integrated positions", "topics": [ "plot_hom_vs_LG" ] }, { "page": "plot_map", "title": "Plot linkage maps", "topics": [ "plot_map" ] }, { "page": "plot_phased_maplist", "title": "Visualise the phased homologue maplist", "topics": [ "plot_phased_maplist" ] }, { "page": "r_LOD_plot", "title": "Plot r versus LOD", "topics": [ "r_LOD_plot" ] }, { "page": "r2_functions", "title": "Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing diploid cross.", "topics": [ "r2_1.0_1.0", "r2_1.0_1.1", "r2_1.1_1.1", "r2_functions" ] }, { "page": "r3_functions", "title": "Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing triploid from a 4x2 or 2x4 cross.", "topics": [ "r3_2_1.0_1.0", "r3_2_1.0_1.1", "r3_2_1.0_1.2", "r3_2_1.2_1.2", "r3_functions" ] }, { "page": "r4_functions", "title": "Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing tetraploid", "topics": [ "r4_functions" ] }, { "page": "r6_functions", "title": "Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid", "topics": [ "r6_functions" ] }, { "page": "screen_for_duplicate_individuals", "title": "Screen for duplicate individuals", "topics": [ "screen_for_duplicate_individuals" ] }, { "page": "screen_for_duplicate_individuals.gp", "title": "Screen for duplicate individuals using weighted genotype probabilities", "topics": [ "screen_for_duplicate_individuals.gp" ] }, { "page": "screen_for_duplicate_markers", "title": "Screen for and remove duplicated markers", "topics": [ "screen_for_duplicate_markers" ] }, { "page": "screen_for_NA_values", "title": "Screen marker data for NA values", "topics": [ "screen_for_NA_values" ] }, { "page": "SN_SN_P1", "title": "A linkage 'data.frame'.", "topics": [ "SN_DN_P1", "SN_DN_P2", "SN_SN_P1", "SN_SN_P2", "SN_SN_P2_triploid", "SN_SS_P1", "SN_SS_P2" ] }, { "page": "SNSN_LOD_deviations", "title": "Identify deviations in LOD scores between pairs of simplex x nulliplex markers", "topics": [ "SNSN_LOD_deviations" ] }, { "page": "test_prefpairing", "title": "Check for and estimate preferential pairing", "topics": [ "test_prefpairing" ] }, { "page": "write_nested_list", "title": "Write out a nested list", "topics": [ "write_nested_list" ] }, { "page": "write_pwd_list", "title": "Write pwd files from a nested list", "topics": [ "write_pwd_list" ] }, { "page": "write.mct", "title": "Write MapChart file", "topics": [ "write.mct" ] }, { "page": "write.pwd", "title": "Write a JoinMap compatible .pwd file from linkage data.frame.", "topics": [ "write.pwd" ] }, { "page": "write.TSNPM", "title": "Write TetraploidSNPMap input file", "topics": [ "write.TSNPM" ] } ], "_rundeps": [ "backports", "base64enc", "bit", "bit64", "boot", "broom", "bslib", "cachem", "checkmate", "class", "cli", "clipr", "cluster", "codetools", "colorspace", "cpp11", "crayon", "data.table", "digest", "doParallel", "dplyr", "e1071", "ellipse", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "foreach", "foreign", "Formula", "fs", "gdata", "generics", "ggplot2", "glmnet", "glue", "gridExtra", "gtable", "gtools", "haven", "highr", "Hmisc", "hms", "htmlTable", 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Bourke, Geert van Geest", "engine": "knitr::rmarkdown", "headings": [ "Table of Contents", "1. A (very) short introduction to R and the polymapR package.", "2. Install polymapR", "3. Logging function calls and output", "4. Data importing", "4.1 Reading in marker dosage data", "But first, a note on polyploid terminology", "4.2 Checking for skewness", "4.3 Running a PCA", "5. Generate summary data", "6. Convert marker dosages to simple segregations; remove non-segregating data", "7. Quality checks on marker data", "7.1 Missing value rate per marker", "7.2 Missing value rate per individual", "7.3 Duplicate individuals", "7.4 Duplicated markers", "8. Simplex x nulliplex markers – defining chromosomes and homologues", "A note on arguments and multi-core processing", "A note on nested lists", "8.1 Using the function overviewSNlinks", "8.2 Using the function cluster_per_LG", "8.3 Cross-ploidy populations (e.g. tetraploid x diploid to give triploid F1)", "9. Assigning SxS and DxN markers and consensus linkage group (LG) names", "10. Assign all other markertypes", "11. Finish the linkage analysis", "12. Marker ordering", "12.1 Creating an integrated chromosomal linkage map", "12.2 Optional: Adding back duplicated markers", "12.3 Phasing an integrated map", "13. Plotting a map", "14. Evaluating map quality", "15. Preferential pairing", "16. QTL analysis", "17. Concluding remarks", "18. References" ], "created": "2017-12-05 17:39:06", "modified": "2025-10-17 16:40:02", "commits": 14 }, { "source": "Vignette_genotype_probabilities.Rmd", "filename": "Vignette_genotype_probabilities.html", "title": "Using genotype probabilities in polymapR", "author": "Peter M. Bourke, Yanlin Liao", "engine": "knitr::rmarkdown", "headings": [ "Table of Contents", "1. Introduction", "2. Importing sample data", "3. Initial mapping steps", "4. Data filtering", "4.1. Quality check on offspring scores", "4.2. Distribution of maximum genotype probabilities", "4.3. Screen for duplicate individuals", "4.4. Screen for duplicate markers", "4.5. Screening for missingness", "5. Marker conversion", "6. Linkage analysis", "6.1 Simplex markers - clustering homologues", "6.2 Higher-dose markers - connecting clustered homologues", "6.3 Marker assignments", "7. Ordering the map", "8. References" ], "created": "2020-07-15 21:30:08", "modified": "2024-01-09 02:43:01", "commits": 5 } ], "_score": 4.064457989226918, "_indexed": true, "_nocasepkg": "polymapr", "_universes": [ "pbourkey" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.7", "date": "2026-05-15T08:30:50.000Z", "distro": "noble", "commit": "2d18f9eac3da5c41765974f4d11a1445d147c701", "fileid": "bf9de48a37003fca032dbb45bfc8b0caf6596f6853877e58b3ae1733fb6f7f7b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pbourkey/actions/runs/25907584982" }, { "r": "4.6.0", "os": "linux", "version": "1.1.7", "date": "2026-05-15T08:31:22.000Z", "distro": "noble", "commit": "2d18f9eac3da5c41765974f4d11a1445d147c701", "fileid": "cf3c4a2ac7fa1bd7a68689889446bb2727155c14b31115d378c1694c0b01e00b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pbourkey/actions/runs/25907584982" }, { "r": "4.5.3", "os": "mac", "version": "1.1.7", "date": "2026-05-15T08:29:27.000Z", "commit": "2d18f9eac3da5c41765974f4d11a1445d147c701", "fileid": "e63e5f3476f6bcf7b5c0980d8623f178edb3866256cf7abcece6d053b9e242ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pbourkey/actions/runs/25907584982" }, { "r": "4.6.0", "os": "mac", "version": "1.1.7", "date": "2026-05-15T08:29:43.000Z", "commit": "2d18f9eac3da5c41765974f4d11a1445d147c701", "fileid": "ffc8a24c5b47cba351b80e672345af34afa41a9aeb38bbc026e7f988bc4164fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pbourkey/actions/runs/25907584982" }, { "r": "4.7.0", "os": "win", "version": "1.1.7", "date": "2026-05-15T08:28:46.000Z", "commit": "2d18f9eac3da5c41765974f4d11a1445d147c701", "fileid": "c9e11ef814aa94f6675dc95db1218edb600af4a1732abde0f0356c768faeab53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pbourkey/actions/runs/25907584982" }, { "r": "4.5.3", "os": "win", "version": "1.1.7", "date": "2026-05-15T08:28:58.000Z", "commit": "2d18f9eac3da5c41765974f4d11a1445d147c701", "fileid": "1b7d25a261b611bc97722450bc17a33f9b712dbd4ab816234f9dc822d677cb52", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pbourkey/actions/runs/25907584982" }, { "r": "4.6.0", "os": "win", "version": "1.1.7", "date": "2026-05-15T08:28:48.000Z", "commit": "2d18f9eac3da5c41765974f4d11a1445d147c701", "fileid": "33abe380755db96477edca63b9a5a730f6346de7005f06e052db2aff0824586d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pbourkey/actions/runs/25907584982" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.7", "date": "2026-06-02T19:39:26.000Z", "commit": "2d18f9eac3da5c41765974f4d11a1445d147c701", "fileid": "418af8aab4578695175dd35a91c2f08ebee68d0e10a40bf67a96d7633e760f4c", "status": "success", "buildurl": "https://github.com/r-universe/pbourkey/actions/runs/25907584982" } ] }