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mappoly
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", "0.4.2") Attach the package and use:
library("mappoly")
Maintained by
Marcelo Mollinari
[Scholar Profile | Author Map]
[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 0.4.2, https://cran.r-project.org/web/packages/mappoly. Accessed 22 Sep. 2026.
Previous versions and publish date:
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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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