Man pages for mmollina/MAPPoly
Genetic Linkage Maps in Autopolyploids
| add_marker | Add a single marker to a map |
| add_md_markers | Add markers to a pre-existing sequence using HMM analysis and... |
| add_mrk_at_tail_ph_list | add a single marker at the tail of a linkage phase list |
| aggregate_matrix | Aggregate matrix cells (lower the resolution by a factor) |
| cache_counts_twopt | Frequency of genotypes for two-point recombination fraction... |
| calc_genoprob | Compute conditional probabilities of the genotypes |
| calc_genoprob_dist | Compute conditional probabilities of the genotypes using... |
| calc_genoprob_error | Compute conditional probabilities of the genotypes using... |
| calc_genoprob_haplo | Compute conditional probabilities of the genotypes given a... |
| calc_genoprob_single_parent | Compute conditional probabilities of the genotype (one... |
| calc_homologprob | Homolog probabilities |
| calc_prefpair_profiles | Preferential pairing profiles |
| cat_phase | cat for phase information |
| check_data_dist_sanity | Checks the consistency of dataset (probability distribution) |
| check_data_dose_sanity | Checks the consistency of dataset (dosage) |
| check_data_sanity | Data sanity check |
| check_if_rf_is_possible | Check if it is possible to estimate the recombination... |
| check_ls_phase | Compare a list of linkage phases and return the markers for... |
| check_pairwise | Check if all pairwise combinations of elements of 'input.seq'... |
| compare_haplotypes | Compare two polyploid haplotypes stored in list format |
| compare_maps | Compare a list of maps |
| concatenate_new_marker | Concatenate new marker |
| concatenate_ph_list | concatenate two linkage phase lists |
| create_map | Create a map with pseudomarkers at a given step |
| cross_simulate | Simulate an autopolyploid full-sib population |
| detect_info_par | Detects which parent is informative |
| dist_prob_to_class | Returns the class with the highest probability in a genotype... |
| draw_cross | Draw simple parental linkage phase configurations |
| draw_phases | Plot the linkage phase configuration given a list of... |
| drop_marker | Remove markers from a map |
| edit_order | Edit sequence ordered by reference genome positions comparing... |
| elim_conf_using_two_pts | Eliminate configurations using two-point information |
| elim_equiv | Eliminates equivalent linkage phase configurations |
| elim_redundant | Eliminate redundant markers |
| est_full_hmm_with_global_error | Re-estimate genetic map given a global genotyping error |
| est_full_hmm_with_prior_prob | Re-estimate genetic map using dosage prior probability... |
| est_haplo_hmm | Estimate a genetic map given a sequence of block markers |
| est_map_haplo_given_genoprob | Estimate a genetic map given a sequence of block markers... |
| est_pairwise_rf | Pairwise two-point analysis |
| est_pairwise_rf2 | Pairwise two-point analysis - RcppParallel version |
| est_rf_hmm | Multipoint analysis using Hidden Markov Models in... |
| est_rf_hmm_sequential | Multipoint analysis using Hidden Markov Models: Sequential... |
| est_rf_hmm_single_phase | Multipoint analysis using Hidden Markov Models (single phase) |
| est_rf_hmm_single_phase_single_parent | Multilocus analysis using Hidden Markov Models (single... |
| export_data_to_polymapR | Export data to 'polymapR' |
| export_map_list | Export a genetic map to a CSV file |
| export_qtlpoly | Export to QTLpoly |
| extract_map | Extract the maker position from an object of class... |
| filter_aneuploid | Filter aneuploid chromosomes from progeny individuals |
| filter_individuals | Filter out individuals |
| filter_map_at_hmm_thres | Filter MAPpoly Map Configurations by Loglikelihood Threshold |
| filter_missing | Filter missing genotypes |
| filter_missing_ind | Filter individuals based on missing genotypes |
| filter_missing_mrk | Filter markers based on missing genotypes |
| filter_non_conforming_classes | Filter non-conforming classes in F1, non double reduced... |
| filter_segregation | Filter markers based on chi-square test |
| find_blocks | Allocate markers into linkage blocks |
| format_rf | Format results from pairwise two-point estimation in C++ |
| framework_map | Design linkage map framework in two steps: i) estimating the... |
| generate_all_link_phase_elim_equivalent | Generate all possible linkage phases in matrix form given the... |
| generate_all_link_phases_elim_equivalent_haplo | Eliminate equivalent linkage phases |
| genetic-mapping-functions | Genetic Mapping Functions |
| genotyping_global_error | Prior probability for genotyping error |
| get_cache_two_pts_from_web | Access a remote server to get Counts for recombinant classes |
| get_counts | Counts for recombinant classes |
| get_counts_all_phases | Counts for recombinant classes |
| get_counts_single_parent | Counts for recombinant classes in a polyploid parent. |
| get_counts_two_parents | Counts for recombinant classes |
| get_dosage_type | Get Dosage Type in a Sequence |
| get_full_info_tail | Get the tail of a marker sequence up to the point where the... |
| get_genomic_order | Get the genomic position of markers in a sequence |
| get_ij | Given a pair of character indicating the numbers i and j :... |
| get_indices_from_selected_phases | Get the indices of selected linkage phases given a threshold |
| get_LOD | Extract the LOD Scores in a "mappoly.map" object |
| get_ols_map | Get weighted ordinary least squared map give a sequence and... |
| get_ph_conf_ret_sh | Given a homology group in matrix form, it returns the number... |
| get_ph_list_subset | subset of a linkage phase list |
| get_rf_from_list | Get the recombination fraction for a sequence of markers... |
| get_rf_from_mat | Get recombination fraction from a matrix |
| get_states_and_emission_single_parent | Get states and emission in one informative parent |
| get_submap | Extract sub-map from map |
| get_tab_mrks | Get table of dosage combinations |
| get_w_m | Get the number of bivalent configurations |
| gg_color_hue | Color pallet ggplot-like |
| group_mappoly | Assign markers to linkage groups |
| hexafake | Simulated autohexaploid dataset. |
| hexafake.geno.dist | Simulated autohexaploid dataset with genotype probabilities. |
| import_data_from_polymapR | Import data from polymapR |
| import_from_updog | Import from updog |
| import_phased_maplist_from_polymapR | Import phased map list from polymapR |
| is.prob.data | Check if Object is a Probability Dataset in MAPpoly |
| loglike_hmm | Multipoint log-likelihood computation |
| ls_linkage_phases | List of linkage phases |
| make_mat_mappoly | Subset recombination fraction matrices |
| make_pairs_mappoly | Subset pairwise recombination fractions |
| make_seq_mappoly | Create a Sequence of Markers |
| mappoly-color-palettes | MAPpoly Color Palettes |
| maps.hexafake | Resulting maps from 'hexafake' |
| mds_mappoly | Estimates loci position using Multidimensional Scaling |
| merge_datasets | Merge datasets |
| merge_maps | Merge two maps |
| merge_parental_maps | Build merged parental maps |
| mrk_chisq_test | Chi-square test |
| msg | Msg function |
| paralell_pairwise_discrete | Parallel Pairwise Discrete Estimation |
| paralell_pairwise_discrete_rcpp | Wrapper function to discrete-based pairwise two-point... |
| paralell_pairwise_probability | Parallel Pairwise Probability Estimation |
| parallel_block | Auxiliary function to estimate a map in a block of markers... |
| perm_pars | N!/2 combination |
| perm_tot | N! combination |
| ph_list_to_matrix | Linkage phase format conversion: list to matrix |
| ph_matrix_to_list | Linkage phase format conversion: matrix to list |
| plot_compare_haplotypes | Plot Two Overlapped Haplotypes |
| plot_genome_vs_map | Physical versus genetic distance |
| plot_GIC | Genotypic information content |
| plot_map_list | Plot a genetic map |
| plot.mappoly.homoprob | Plots mappoly.homoprob |
| plot_mappoly.map2 | Plot object mappoly.map2 |
| plot.mappoly.prefpair.profiles | Plots mappoly.prefpair.profiles |
| plot_mrk_info | Plot marker information |
| plot_one_map | plot a single linkage group with no phase |
| plot_progeny_dosage_change | Display genotypes imputed or changed by the HMM chain given a... |
| poly_hmm_est | Estimate genetic map using as input the probability... |
| prepare_map | prepare maps for plot |
| print_mrk | Summary of a set of markers |
| print_ph | cat for graphical representation of the phases |
| read_fitpoly | Data Input in fitPoly format |
| read_geno | Data Input |
| read_geno_csv | Data Input in CSV format |
| read_geno_prob | Data Input |
| read_vcf | Data Input VCF |
| reest_rf | Re-estimate the recombination fractions in a genetic map |
| rev_map | Reverse map |
| rf_list_to_matrix | Recombination fraction list to matrix |
| rf_snp_filter | Remove markers that do not meet a LOD criteria |
| sample_data | Random sampling of dataset |
| segreg_poly | Polysomic segregation frequency |
| select_rf | Select rf and lod based on thresholds |
| sim_cross_one_informative_parent | Simulate mapping population (one parent) |
| sim_cross_two_informative_parents | Simulate mapping population (tow parents) |
| sim_homologous | Simulate homology groups |
| solcap.dose.map | Resulting maps from 'tetra.solcap' |
| solcap.err.map | Resulting maps from 'tetra.solcap' |
| solcap.mds.map | Resulting maps from 'tetra.solcap' |
| solcap.prior.map | Resulting maps from 'tetra.solcap.geno.dist' |
| split_and_rephase | Divides map in sub-maps and re-phase them |
| split_mappoly | Split map into sub maps given a gap threshold |
| summary_maps | Summary maps |
| table_to_mappoly | Conversion of data.frame to mappoly.data |
| tetra.solcap | Autotetraploid potato dataset. |
| tetra.solcap.geno.dist | Autotetraploid potato dataset with genotype probabilities. |
| update_framework_map | Add markers that are informative in both parents using HMM... |
| update_map | Update map |
| update_missing | Update missing information |
| update_ph_list_at_hmm_thres | makes a phase list from map, selecting only configurations... |
| v_2_m | Conversion: vector to matrix |
