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mappoly  

Genetic Linkage Maps in Autopolyploids
View on CRAN: Click here


Download and install mappoly package within the R console
Install from CRAN:
install.packages("mappoly")

Install from Github:
library("remotes")
install_github("cran/mappoly")

Install by package version:
library("remotes")
install_version("mappoly", "0.4.1")



Attach the package and use:
library("mappoly")
Maintained by
Marcelo Mollinari
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-10-10
Latest Update: 2024-03-06
Description:
Construction of genetic maps in autopolyploid full-sib populations. Uses pairwise recombination fraction estimation as the first source of information to sequentially position allelic variants in specific homologous chromosomes. For situations where pairwise analysis has limited power, the algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM). For more detail, please see Mollinari and Garcia (2019) and Mollinari et al. (2020) .
How to cite:
Marcelo Mollinari (2020). mappoly: Genetic Linkage Maps in Autopolyploids. R package version 0.4.1, https://cran.r-project.org/web/packages/mappoly. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.2.0 (2020-10-10 12:00), 0.2.1 (2020-11-23 11:50), 0.2.3 (2021-04-20 12:00), 0.3.0 (2022-01-11 10:22), 0.3.1 (2022-07-06 11:30), 0.3.2 (2022-12-02 09:00), 0.3.3 (2023-01-05 21:10), 0.4.0 (2024-02-18 00:30)
Other packages that cited mappoly R package
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Other R packages that mappoly depends, imports, suggests or enhances
Complete documentation for mappoly
Functions, R codes and Examples using the mappoly R package
Some associated functions: add_marker . add_mrk_at_tail_ph_list . aggregate_matrix . cache_counts_twopt . calc_genoprob . calc_genoprob_dist . calc_genoprob_error . calc_genoprob_haplo . calc_genoprob_one_parent . calc_homologprob . calc_prefpair_profiles . cat_phase . check_data_dist_sanity . check_data_dose_sanity . check_data_sanity . check_if_rf_is_possible . check_ls_phase . check_pairwise . compare_haplotypes . compare_maps . concatenate_new_marker . concatenate_ph_list . create_map . dist_prob_to_class . draw_cross . draw_phases . drop_marker . elim_conf_using_two_pts . elim_equiv . elim_redundant . est_full_hmm_with_global_error . est_full_hmm_with_prior_prob . est_haplo_hmm . est_map_haplo_given_genoprob . est_pairwise_rf . est_pairwise_rf2 . est_rf_hmm . est_rf_hmm_sequential . est_rf_hmm_single . est_rf_hmm_single_one_parent . export_data_to_polymapR . export_map_list . export_qtlpoly . extract_map . filter_individuals . filter_map_at_hmm_thres . filter_missing . filter_missing_ind . filter_missing_mrk . filter_non_conforming_classes . filter_segregation . find_blocks . format_rf . generate_all_link_phase_elim_equivalent . generate_all_link_phases_elim_equivalent_haplo . genotyping_global_error . get_LOD . get_cache_two_pts_from_web . get_counts . get_counts_all_phases . get_counts_one_parent . get_counts_two_parents . get_dosage_type . get_full_info_tail . get_genomic_order . get_ij . get_indices_from_selected_phases . get_ols_map . get_ph_conf_ret_sh . get_ph_list_subset . get_rf_from_list . get_rf_from_mat . get_states_and_emission_one_parent . get_submap . get_tab_mrks . get_w_m . gg_color_hue . group_mappoly . hexafake.geno.dist . hexafake . imf_h . imf_k . imf_m . import_data_from_polymapR . import_from_updog . import_phased_maplist_from_polymapR . is.prob.data . loglike_hmm . ls_linkage_phases . make_mat_mappoly . make_pairs_mappoly . make_seq_mappoly . maps.hexafake . mds_mappoly . merge_datasets . merge_maps . mf_h . mf_k . mf_m . mp_pallet1 . mp_pallet2 . mp_pallet3 . mrk_chisq_test . msg . paralell_pairwise_discrete . paralell_pairwise_discrete_rcpp . paralell_pairwise_probability . parallel_block . perm_pars . perm_tot . ph_list_to_matrix . ph_matrix_to_list . plot.mappoly.homoprob . plot.mappoly.prefpair.profiles . plot_GIC . plot_compare_haplotypes . plot_genome_vs_map . plot_map_list . plot_mrk_info . plot_one_map . poly_cross_simulate . poly_hmm_est . prepare_map . print_mrk . print_ph . read_fitpoly . read_geno . read_geno_csv . read_geno_prob . read_vcf . reest_rf . rev_map . rf_list_to_matrix . rf_snp_filter . sample_data . segreg_poly . select_rf . sim_cross_one_informative_parent . sim_cross_two_informative_parents . sim_homologous . solcap.dose.map . solcap.err.map . solcap.mds.map . solcap.prior.map . split_and_rephase . split_mappoly . summary_maps . table_to_mappoly . tetra.solcap.geno.dist . tetra.solcap . update_map . update_missing . update_ph_list_at_hmm_thres . v_2_m . 
Some associated R codes: RcppExports.R . cache_twopts.R . calc_genoprob.R . calc_genoprob_dist.R . calc_genoprob_error.R . calc_genoprob_one_parent.R . check_phase_configurations.R . data.R . eliminate_redundant.R . est_map_hmm.R . export_map_list.R . export_qtlpoly.R . filters.R . find_blocks.R . get_counts.R . get_counts_from_web.R . get_submap.R . group.R . haplotype_map_utils.R . homolog_probs.R . import_from_polymapR.R . import_from_updog.R . loglike_hmm.R . make_mat.R . make_pairs.R . make_seq.R . marker_info.R . mds.R . merge_maps.R . one_paprent_single_map_hmm.R . pairwise_rf.R . plot_genome_vs_map.R . plot_map_list.R . poly_cross_simulate.R . preferential_pairing.R . prior_dist_hmm.R . read_fitpoly.R . read_mappoly.R . read_mappoly_csv.R . read_mappoly_prob.R . read_mappoly_vcf.R . reest_map_error.R . reestimate_map.R . rf_list_to_matrix.R . segreg_poly.R . sim_homologous.R . simulation_utils.R . single_map_hmm.R . split_and_rephase.R . utils.R . zzz.R .  Full mappoly package functions and examples
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