Other packages > Find by keyword >

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
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
View mappoly citation profile
Other R packages that mappoly depends, imports, suggests or enhances
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
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

mistral  
Methods in Structural Reliability
Various reliability analysis methods for rare event inference (computing failure probability and qua ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
steepness  
Testing Steepness of Dominance Hierarchies
The steepness package computes steepness as a property of dominance hierarchies. Steepness is define ...
Download / Learn more Package Citations See dependency  
rdbnomics  
Download DBnomics Data
R access to hundreds of millions data series from DBnomics API (). ...
Download / Learn more Package Citations See dependency  
critpath  
Setting the Critical Path in Project Management
Solving the problem of project management using CPM (Critical Path Method), PERT (Program Evaluation ...
Download / Learn more Package Citations See dependency  
ftaproxim  
Fault Tree Analysis Based on Proxel Simulation
Calculation and plotting of instantaneous unavailabilities of basic events along with the top event ...
Download / Learn more Package Citations See dependency  

22,114

R Packages

188,080

Dependencies

55,244

Author Associations

22,115

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net. Contact Us / Suggestions / Concerns