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create_data_bins function", "topics": [ "add_redundants" ] }, { "page": "Bonferroni_alpha", "title": "Calculates individual significance level to be used to achieve a global alpha (with Bonferroni)", "topics": [ "Bonferroni_alpha" ] }, { "page": "check_data", "title": "Onemap object sanity check", "topics": [ "check_data" ] }, { "page": "check_twopts", "title": "Twopts object sanity check", "topics": [ "check_twopts" ] }, { "page": "combine_onemap", "title": "Combine OneMap datasets", "topics": [ "combine_onemap" ] }, { "page": "compare", "title": "Compare all possible orders (exhaustive search) for a given sequence of markers", "topics": [ "compare" ] }, { "page": "create_data_bins", "title": "New dataset based on bins", "topics": [ "create_data_bins" ] }, { "page": "create_dataframe_for_plot_outcross", "title": "Create a dataframe suitable for a ggplot2 graphic", "topics": [ "create_dataframe_for_plot_outcross" ] }, { "page": "create_depths_profile", "title": "Create database and ggplot graphic of allele reads depths", "topics": [ "create_depths_profile" ] }, { "page": "create_probs", "title": "Build genotype probabilities matrix for hmm", "topics": [ "create_probs" ] }, { "page": "draw_map", "title": "Draw a genetic map", "topics": [ "draw_map" ] }, { "page": "draw_map2", "title": "Draw a linkage map", "topics": [ "draw_map2" ] }, { "page": "drop_marker", "title": "Creates a new sequence by dropping markers.", "topics": [ "drop_marker" ] }, { "page": "edit_order_onemap", "title": "Edit sequence ordered by reference genome positions comparing to another set order", "topics": [ "edit_order_onemap" ] }, { "page": "empty_onemap_obj", "title": "Produce empty object to avoid code break. Function for internal purpose.", "topics": [ "empty_onemap_obj" ] }, { "page": "export_mappoly_genoprob", "title": "Export genotype probabilities in MAPpoly format (input for QTLpoly)", "topics": [ "export_mappoly_genoprob" ] }, { "page": "export_viewpoly", "title": "Export OneMap maps to be visualized in VIEWpoly", "topics": [ "export_viewpoly" ] }, { "page": "extract_depth", "title": "Extract allele counts of progeny and parents of vcf file", "topics": [ "extract_depth" ] }, { "page": "filter_2pts_gaps", "title": "Filter markers based on 2pts distance", "topics": [ "filter_2pts_gaps" ] }, { "page": "filter_missing", "title": "Filter markers according with a missing data threshold", "topics": [ "filter_missing" ] }, { "page": "filter_prob", "title": "Function filter genotypes by genotype probability", "topics": [ "filter_prob" ] }, { "page": "find_bins", "title": "Allocate markers into bins", "topics": [ "find_bins" ] }, { "page": "generate_overlapping_batches", "title": "Function to divide the sequence in batches with user defined size", "topics": [ "generate_overlapping_batches" ] }, { "page": "group", "title": "Assign markers to linkage groups", "topics": [ "group" ] }, { "page": "group_seq", "title": "Assign markers to preexisting linkage groups", "topics": [ "group_seq" ] }, { "page": "group_upgma", "title": "Assign markers to linkage groups", "topics": [ "group_upgma" ] }, { "page": "haldane", "title": "Apply Haldane mapping function", "topics": [ "haldane" ] }, { "page": "keep_only_selected_mks", "title": "Keep in the onemap and twopts object only markers in the sequences", "topics": [ "keep_only_selected_mks" ] }, { "page": "kosambi", "title": "Apply Kosambi mapping function", "topics": [ "kosambi" ] }, { "page": "load_onemap_sequences", "title": "Load list of sequences saved by save_onemap_sequences", "topics": [ "load_onemap_sequences" ] }, { "page": "make_seq", "title": "Create a sequence of markers based on other OneMap object types", "topics": [ "make_seq" ] }, { "page": "map", "title": "Construct the linkage map for a sequence of markers", "topics": [ "map" ] }, { "page": "map_avoid_unlinked", "title": "Repeat HMM if map find unlinked marker", "topics": [ "map_avoid_unlinked" ] }, { "page": "map_overlapping_batches", "title": "Mapping overlapping batches", "topics": [ "map_overlapping_batches" ] }, { "page": "map_save_ram", "title": "Perform map using background objects with only selected markers. It saves ram memory during the procedure. It is useful if dealing with many markers in total data set.", "topics": [ "map_save_ram" ] }, { "page": "mapmaker_example_f2", "title": "Simulated data from a F2 population", "topics": [ "mapmaker_example_f2" ] }, { "page": "marker_type", "title": "Informs the segregation patterns of markers", "topics": [ "marker_type" ] }, { "page": "mds_onemap", "title": "OneMap interface with MDSMap package with option for multipoint distances estimation", "topics": [ "mds_onemap" ] }, { "page": "onemap_example_bc", "title": "Simulated data from a backcross population", "topics": [ "onemap_example_bc" ] }, { "page": "onemap_example_f2", "title": "Simulated data from a F2 population", "topics": [ "onemap_example_f2" ] }, { "page": "onemap_example_out", "title": "Data from a full-sib family derived from two outbred parents", "topics": [ "onemap_example_out" ] }, { "page": "onemap_example_riself", "title": "Simulated data from a RIL population produced by selfing.", "topics": [ "onemap_example_riself" ] }, { "page": "onemap_read_vcfR", "title": "Convert vcf file to onemap object", "topics": [ "onemap_read_vcfR" ] }, { "page": "ord_by_geno", "title": "Order the markers in a sequence using the genomic position", "topics": [ "ord_by_geno" ] }, { "page": "order_seq", "title": "Search for the best order of markers combining compare and try_seq functions", "topics": [ "order_seq" ] }, { "page": "parents_haplotypes", "title": "Generates data.frame with parents estimated haplotypes", "topics": [ "parents_haplotypes" ] }, { "page": "pick_batch_sizes", "title": "Picking optimal batch size values", "topics": [ "pick_batch_sizes" ] }, { "page": "plot_by_segreg_type", "title": "Draw a graphic showing the number of markers of each segregation pattern.", "topics": [ "plot_by_segreg_type" ] }, { "page": "plot_genome_vs_cm", "title": "Draws a physical vs cM map", "topics": [ "plot_genome_vs_cm" ] }, { "page": "plot.onemap", "title": "Draw a graphic of raw data for any OneMap population", "topics": [ "plot.onemap" ] }, { "page": "plot.onemap_progeny_haplotypes", "title": "Plots progeny haplotypes", "topics": [ "plot.onemap_progeny_haplotypes" ] }, { "page": "plot.onemap_progeny_haplotypes_counts", "title": "Plot recombination breakpoints counts for each individual", "topics": [ "plot.onemap_progeny_haplotypes_counts" ] }, { "page": "plot.onemap_segreg_test", "title": "Plot p-values for chi-square tests of expected segregation", "topics": [ "plot.onemap_segreg_test" ] }, { "page": "print.compare", "title": "print method for object class 'compare'", "topics": [ "print.compare" ] }, { "page": "print.onemap", "title": "Print method for object class 'onemap'", "topics": [ "print.onemap" ] }, { "page": "print.onemap_bin", "title": "print method for object class 'onemap_bin'", "topics": [ "print.onemap_bin" ] }, { "page": "print.onemap_segreg_test", "title": "Show the results of segregation tests", "topics": [ "print.onemap_segreg_test" ] }, { "page": "print.order", "title": "Print order_seq object", "topics": [ "print.order" ] }, { "page": "print.sequence", "title": "Print method for object class 'sequence'", "topics": [ "print.sequence" ] }, { "page": "progeny_haplotypes", "title": "Generate data.frame with genotypes estimated by HMM and its probabilities", "topics": [ "progeny_haplotypes" ] }, { "page": "progeny_haplotypes_counts", "title": "Plot number of breakpoints by individuals", "topics": [ "progeny_haplotypes_counts" ] }, { "page": "rcd", "title": "Rapid Chain Delineation", "topics": [ "rcd" ] }, { "page": "read_mapmaker", "title": "Read data from a Mapmaker raw file", "topics": [ "read_mapmaker" ] }, { "page": "read_onemap", "title": "Read data from all types of progenies supported by OneMap", "topics": [ "read_onemap" ] }, { "page": "record", "title": "Recombination Counting and Ordering", "topics": [ "record" ] }, { "page": "remove_inds", "title": "Remove individuals from the onemap object", "topics": [ "remove_inds" ] }, { "page": "rf_2pts", "title": "Two-point analysis between genetic markers", "topics": [ "rf_2pts" ] }, { "page": "rf_graph_table", "title": "Plots pairwise recombination fractions and LOD Scores in a heatmap", "topics": [ "rf_graph_table" ] }, { "page": "rf_snp_filter_onemap", "title": "Filter markers according with a two-points recombination fraction and LOD threshold. Adapted from MAPpoly.", "topics": [ "rf_snp_filter_onemap" ] }, { "page": "ripple_seq", "title": "Compares and displays plausible alternative orders for a given linkage group", "topics": [ "ripple_seq" ] }, { "page": "rm_dupli_mks", "title": "Remove duplicated markers keeping the one with less missing data", "topics": [ "rm_dupli_mks" ] }, { "page": "save_onemap_sequences", "title": "Save a list of onemap sequence objects", "topics": [ "save_onemap_sequences" ] }, { "page": "seeded_map", "title": "Construct the linkage map for a sequence of markers after seeding phases", "topics": [ "seeded_map" ] }, { "page": "select_segreg", "title": "Show markers with/without segregation distortion", "topics": [ "select_segreg" ] }, { "page": "seq_by_type", "title": "Extract marker number by name", "topics": [ "seq_by_type" ] }, { "page": "seriation", "title": "Seriation", "topics": [ "seriation" ] }, { "page": "set_map_fun", "title": "Defines the default mapping function", "topics": [ "set_map_fun" 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