API for mappoly
Genetic Linkage Maps in Autopolyploids
| Global functions | |
|---|---|
| .mappoly_data_skeleton | Source code |
| .mappoly_map_skeleton | Source code |
| .onAttach | Source code |
| .vcf_get_depth | Source code |
| .vcf_get_ploidy | Source code |
| .vcf_get_probabilities | Source code |
| .vcf_transform_dosage | Source code |
| StartWelcomeMessage | Source code |
| add_marker | Man page Source code |
| add_md_markers | Man page Source code |
| add_mrk_at_tail_ph_list | Man page Source code |
| aggregate_matrix | Man page Source code |
| cache_counts_twopt | Man page Source code |
| calc_genoprob | Man page Source code |
| calc_genoprob_cpp | Source code |
| calc_genoprob_dist | Man page Source code |
| calc_genoprob_error | Man page Source code |
| calc_genoprob_haplo | Man page Source code |
| calc_genoprob_single_parent | Man page Source code |
| calc_genprob_haplo_cpp | Source code |
| calc_genprob_haplo_highprec_cpp | Source code |
| calc_homologprob | Man page Source code |
| calc_prefpair_profiles | Man page Source code |
| cat_phase | Man page Source code |
| check_data_dist_sanity | Man page Source code |
| check_data_dose_sanity | Man page Source code |
| check_data_sanity | Man page Source code |
| check_if_rf_is_possible | Man page Source code |
| check_ls_phase | Man page Source code |
| check_pairwise | Man page Source code |
| compare_haplotypes | Man page Source code |
| compare_maps | Man page Source code |
| concatenate_new_marker | Man page Source code |
| concatenate_ph_list | Man page Source code |
| create_map | Man page Source code |
| cross_simulate | Man page Source code |
| detect_info_par | Man page Source code |
| dist_prob_to_class | Man page Source code |
| draw_cross | Man page Source code |
| draw_phases | Man page Source code |
| drop_marker | Man page Source code |
| edit_order | Man page Source code |
| elim_conf_using_two_pts | Man page Source code |
| elim_equiv | Man page Source code |
| elim_redundant | Man page Source code |
| est_full_hmm_with_global_error | Man page Source code |
| est_full_hmm_with_prior_prob | Man page Source code |
| est_haplo_hmm | Man page Source code |
| est_map_haplo_given_genoprob | Man page Source code |
| est_pairwise_rf | Man page Source code |
| est_pairwise_rf2 | Man page Source code |
| est_rf_hmm | Man page Source code |
| est_rf_hmm_sequential | Man page Source code |
| est_rf_hmm_single_phase | Man page Source code |
| est_rf_hmm_single_phase_single_parent | Man page Source code |
| export_data_to_polymapR | Man page Source code |
| export_map_list | Man page Source code |
| export_qtlpoly | Man page Source code |
| extract_map | Man page Source code |
| filter_aneuploid | Man page Source code |
| filter_individuals | Man page Source code |
| filter_map_at_hmm_thres | Man page Source code |
| filter_missing | Man page Source code |
| filter_missing_ind | Man page Source code |
| filter_missing_mrk | Man page Source code |
| filter_non_conforming_classes | Man page Source code |
| filter_segregation | Man page Source code |
| find_blocks | Man page Source code |
| format_rf | Man page Source code |
| framework_map | Man page Source code |
| generate_all_link_phase_elim_equivalent | Man page Source code |
| generate_all_link_phases_elim_equivalent_haplo | Man page Source code |
| genetic-mapping-functions | Man page |
| genotyping_global_error | Man page Source code |
| get_LOD | Man page Source code |
| get_cache_two_pts_from_web | Man page Source code |
| get_counts | Man page Source code |
| get_counts_all_phases | Man page Source code |
| get_counts_single_parent | Man page Source code |
| get_counts_two_parents | Man page Source code |
| get_dosage_type | Man page Source code |
| get_full_info_tail | Man page Source code |
| get_genomic_order | Man page Source code |
| get_ij | Man page Source code |
| get_indices_from_selected_phases | Man page Source code |
| get_ols_map | Man page Source code |
| get_ph_conf_ret_sh | Man page Source code |
| get_ph_list_subset | Man page Source code |
| get_rf_from_list | Man page Source code |
| get_rf_from_mat | Man page Source code |
| get_states_and_emission_single_parent | Man page Source code |
| get_submap | Man page Source code |
| get_tab_mrks | Man page Source code |
| get_w_m | Man page Source code |
| gg_color_hue | Man page Source code |
| group_mappoly | Man page Source code |
| hexafake | Man page |
| hexafake.geno.dist | Man page |
| imf_h | Man page Source code |
| imf_k | Man page Source code |
| imf_m | Man page Source code |
| import_data_from_polymapR | Man page Source code |
| import_from_updog | Man page Source code |
| import_phased_maplist_from_polymapR | Man page Source code |
| is.prob.data | Man page Source code |
| loglike_hmm | Man page Source code |
| loglike_hmm_cpp | Source code |
| ls_linkage_phases | Man page Source code |
| make_mat_mappoly | Man page Source code |
| make_pairs_mappoly | Man page Source code |
| make_seq_mappoly | Man page Source code |
| mappoly-color-palettes | Man page |
| maps.hexafake | Man page |
| mds_mappoly | Man page Source code |
| merge_datasets | Man page Source code |
| merge_maps | Man page Source code |
| merge_parental_maps | Man page Source code |
| mf_h | Man page Source code |
| mf_k | Man page Source code |
| mf_m | Man page Source code |
| mp_pallet1 | Man page |
| mp_pallet2 | Man page |
| mp_pallet3 | Man page |
| mrk_chisq_test | Man page Source code |
| msg | Man page Source code |
| paralell_pairwise_discrete | Man page Source code |
| paralell_pairwise_discrete_rcpp | Man page Source code |
| paralell_pairwise_probability | Man page Source code |
| parallel_block | Man page Source code |
| perm_pars | Man page Source code |
| perm_tot | Man page Source code |
| ph_list_to_matrix | Man page Source code |
| ph_matrix_to_list | Man page Source code |
| plot.mappoly.data | Man page Source code |
| plot.mappoly.geno.ord | Man page Source code |
| plot.mappoly.group | Source code |
| plot.mappoly.homoprob | Man page Source code |
| plot.mappoly.map | Man page Source code |
| plot.mappoly.pcmap3d | Source code |
| plot.mappoly.prefpair.profiles | Man page Source code |
| plot.mappoly.rf.matrix | Man page Source code |
| plot.mappoly.sequence | Man page Source code |
| plot.mappoly.twopt | Source code |
| plot.mappoly.unique.seq | Source code |
| plot.two.pts.linkage.phases | Man page Source code |
| plot_GIC | Man page Source code |
| plot_compare_haplotypes | Man page Source code |
| plot_genome_vs_map | Man page Source code |
| plot_map_list | Man page Source code |
| plot_mappoly.map2 | Man page Source code |
| plot_mrk_info | Man page Source code |
| plot_one_map | Man page Source code |
| plot_progeny_dosage_change | Man page Source code |
| poly_hmm_est | Man page Source code |
| prepare_map | Man page Source code |
| print.cache.info | Source code |
| print.mappoly.data | Man page Source code |
| print.mappoly.geno.ord | Man page Source code |
| print.mappoly.genoprob | Source code |
| print.mappoly.group | Source code |
| print.mappoly.homoprob | Source code |
| print.mappoly.map | Man page Source code |
| print.mappoly.pcmap | Man page Source code |
| print.mappoly.pcmap3d | Man page Source code |
| print.mappoly.prefpair.profiles | Source code |
| print.mappoly.rf.matrix | Man page Source code |
| print.mappoly.sequence | Man page Source code |
| print.mappoly.twopt | Source code |
| print.mappoly.unique.seq | Source code |
| print.two.pts.linkage.phases | Man page Source code |
| print_mrk | Man page Source code |
| print_ph | Man page Source code |
| read_fitpoly | Man page Source code |
| read_geno | Man page Source code |
| read_geno_csv | Man page Source code |
| read_geno_prob | Man page Source code |
| read_vcf | Man page Source code |
| reest_rf | Man page Source code |
| rem_mrk_clusters | Source code |
| rev_map | Man page Source code |
| rf_list_to_matrix | Man page Source code |
| rf_snp_filter | Man page Source code |
| sample_data | Man page Source code |
| segreg_poly | Man page Source code |
| select_rf | Man page Source code |
| sim_cross_one_informative_parent | Man page Source code |
| sim_cross_two_informative_parents | Man page Source code |
| sim_homologous | Man page Source code |
| solcap.dose.map | Man page |
| solcap.err.map | Man page |
| solcap.mds.map | Man page |
| solcap.prior.map | Man page |
| split_and_rephase | Man page Source code |
| split_mappoly | Man page Source code |
| summary_maps | Man page Source code |
| table_to_mappoly | Man page Source code |
| tetra.solcap | Man page |
| tetra.solcap.geno.dist | Man page |
| text_col | Source code |
| update_framework_map | Man page Source code |
| update_map | Man page Source code |
| update_missing | Man page Source code |
| update_ph_list_at_hmm_thres | Man page Source code |
| v_2_m | Man page Source code |
