Files in mappoly

Genetic Linkage Maps in Autopolyploids

NEWS.md README.md R/read_mappoly.R R/RcppExports.R R/find_blocks.R R/reestimate_map.R R/get_submap.R R/single_paprent_single_phase_hmm.R R/export_map_list.R R/add_drop.R R/loglike_hmm.R R/plot_genome_vs_map.R R/single_map_hmm.R R/marker_info.R R/segreg_poly.R R/read_mappoly_vcf.R R/make_mat.R R/group.R R/filters.R R/calc_genoprob.R R/data.R R/get_counts.R R/build_map_by_steps.R R/reest_map_error.R R/read_mappoly_csv.R R/simulation_utils.R R/export_qtlpoly.R R/check_phase_configurations.R R/calc_genoprob_error.R R/make_pairs.R R/est_map_hmm.R R/import_from_polymapR.R R/cache_twopts.R R/pairwise_rf.R R/homolog_probs.R R/split_and_rephase.R R/rf_list_to_matrix.R R/import_from_updog.R R/get_counts_from_web.R R/calc_genoprob_dist.R R/merge_maps.R R/plot_progeny_dosage_change.R R/read_fitpoly.R R/make_seq.R R/plot_map_list.R R/mds.R R/zzz.R R/prior_dist_hmm.R R/sim_homologous.R R/haplotype_map_utils.R R/preferential_pairing.R R/read_mappoly_prob.R R/eliminate_redundant.R R/utils.R R/cross_simulate.R R/calc_genoprob_single_parent.R inst/doc/mappoly_startguide.Rmd inst/doc/mappoly_startguide.R vignettes/mappoly_startguide.Rmd man/est_rf_hmm_sequential.Rd man/maps.hexafake.Rd man/sample_data.Rd man/parallel_block.Rd man/reest_rf.Rd man/get_counts_two_parents.Rd man/mrk_chisq_test.Rd man/get_LOD.Rd man/msg.Rd man/sim_homologous.Rd man/print_ph.Rd man/get_genomic_order.Rd man/calc_homologprob.Rd man/est_pairwise_rf.Rd man/filter_individuals.Rd man/filter_aneuploid.Rd man/est_pairwise_rf2.Rd man/solcap.mds.map.Rd man/get_states_and_emission_single_parent.Rd man/segreg_poly.Rd man/paralell_pairwise_probability.Rd man/get_full_info_tail.Rd man/paralell_pairwise_discrete_rcpp.Rd man/drop_marker.Rd man/filter_non_conforming_classes.Rd man/ph_matrix_to_list.Rd man/filter_missing.Rd man/paralell_pairwise_discrete.Rd man/aggregate_matrix.Rd man/concatenate_new_marker.Rd man/find_blocks.Rd man/calc_genoprob_single_parent.Rd man/est_rf_hmm_single_phase_single_parent.Rd man/export_map_list.Rd man/make_pairs_mappoly.Rd man/solcap.err.map.Rd man/plot_genome_vs_map.Rd man/sim_cross_one_informative_parent.Rd man/plot_GIC.Rd man/get_ph_list_subset.Rd man/compare_maps.Rd man/solcap.prior.map.Rd man/read_geno.Rd man/add_marker.Rd man/update_framework_map.Rd man/est_rf_hmm.Rd man/read_geno_prob.Rd man/check_ls_phase.Rd man/merge_maps.Rd man/import_data_from_polymapR.Rd man/rf_list_to_matrix.Rd man/est_full_hmm_with_prior_prob.Rd man/table_to_mappoly.Rd man/calc_genoprob.Rd man/compare_haplotypes.Rd man/make_mat_mappoly.Rd man/perm_tot.Rd man/get_w_m.Rd man/sim_cross_two_informative_parents.Rd man/is.prob.data.Rd man/plot_one_map.Rd man/extract_map.Rd man/plot_compare_haplotypes.Rd man/get_ph_conf_ret_sh.Rd man/elim_redundant.Rd man/get_dosage_type.Rd man/filter_missing_ind.Rd man/split_mappoly.Rd man/filter_segregation.Rd man/generate_all_link_phases_elim_equivalent_haplo.Rd man/plot.mappoly.homoprob.Rd man/create_map.Rd man/make_seq_mappoly.Rd man/filter_map_at_hmm_thres.Rd man/plot.mappoly.prefpair.profiles.Rd man/genotyping_global_error.Rd man/read_vcf.Rd man/check_data_sanity.Rd man/calc_genoprob_error.Rd man/read_geno_csv.Rd man/est_full_hmm_with_global_error.Rd man/plot_mrk_info.Rd man/perm_pars.Rd man/draw_phases.Rd man/check_data_dose_sanity.Rd man/draw_cross.Rd man/get_cache_two_pts_from_web.Rd man/concatenate_ph_list.Rd man/select_rf.Rd man/mappoly-color-palettes.Rd man/plot_map_list.Rd man/print_mrk.Rd man/gg_color_hue.Rd man/import_from_updog.Rd man/hexafake.Rd man/merge_parental_maps.Rd man/est_haplo_hmm.Rd man/update_ph_list_at_hmm_thres.Rd man/calc_prefpair_profiles.Rd man/genetic-mapping-functions.Rd man/framework_map.Rd man/get_ij.Rd man/get_indices_from_selected_phases.Rd man/get_tab_mrks.Rd man/plot_mappoly.map2.Rd man/v_2_m.Rd man/tetra.solcap.geno.dist.Rd man/est_map_haplo_given_genoprob.Rd man/cache_counts_twopt.Rd man/check_if_rf_is_possible.Rd man/prepare_map.Rd man/dist_prob_to_class.Rd man/add_md_markers.Rd man/get_counts_single_parent.Rd man/summary_maps.Rd man/cross_simulate.Rd man/export_qtlpoly.Rd man/get_rf_from_list.Rd man/update_missing.Rd man/get_rf_from_mat.Rd man/hexafake.geno.dist.Rd man/calc_genoprob_haplo.Rd man/get_counts.Rd man/ls_linkage_phases.Rd man/group_mappoly.Rd man/elim_conf_using_two_pts.Rd man/update_map.Rd man/get_submap.Rd man/import_phased_maplist_from_polymapR.Rd man/get_counts_all_phases.Rd man/calc_genoprob_dist.Rd man/est_rf_hmm_single_phase.Rd man/ph_list_to_matrix.Rd man/generate_all_link_phase_elim_equivalent.Rd man/poly_hmm_est.Rd man/check_pairwise.Rd man/cat_phase.Rd man/loglike_hmm.Rd man/elim_equiv.Rd man/rev_map.Rd man/format_rf.Rd man/filter_missing_mrk.Rd man/split_and_rephase.Rd man/get_ols_map.Rd man/export_data_to_polymapR.Rd man/plot_progeny_dosage_change.Rd man/read_fitpoly.Rd man/add_mrk_at_tail_ph_list.Rd man/rf_snp_filter.Rd man/edit_order.Rd man/tetra.solcap.Rd man/solcap.dose.map.Rd man/merge_datasets.Rd man/mds_mappoly.Rd man/detect_info_par.Rd man/check_data_dist_sanity.Rd