Genetic Linkage Maps in Autopolyploids
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Documentation for package ‘mappoly’ version 0.4.1
Help Pages
| add_marker | Add a single marker to a map |
| cache_counts_twopt | Frequency of genotypes for two-point recombination fraction estimation |
| calc_genoprob | Compute conditional probabilities of the genotypes |
| calc_genoprob_dist | Compute conditional probabilities of the genotypes using probability distribution of dosages |
| calc_genoprob_error | Compute conditional probabilities of the genotypes using global error |
| calc_genoprob_single_parent | Compute conditional probabilities of the genotype (one informative parent) |
| calc_homologprob | Homolog probabilities |
| calc_prefpair_profiles | Preferential pairing profiles |
| check_data_sanity | Data sanity check |
| compare_maps | Compare a list of maps |
| cross_simulate | Simulate an autopolyploid full-sib population |
| detect_info_par | Detects which parent is informative |
| drop_marker | Remove markers from a map |
| edit_order | Edit sequence ordered by reference genome positions comparing to another set order |
| 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 distribution |
| 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 autopolyploids |
| est_rf_hmm_sequential | Multipoint analysis using Hidden Markov Models: Sequential phase elimination |
| 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 'mappoly.map' |
| filter_aneuploid | Filter aneuploid chromosomes from progeny individuals |
| filter_individuals | Filter out individuals |
| filter_missing | Filter missing genotypes |
| filter_segregation | Filter markers based on chi-square test |
| find_blocks | Allocate markers into linkage blocks |
| framework_map | Design linkage map framework in two steps: i) estimating the recombination fraction with HMM approach for each parent separately using only markers segregating individually (e.g. map 1 - P1:3 x P2:0, P1: 2x4; map 2 - P1:0 x P2:3, P1:4 x P2:2); ii) merging both maps and re-estimate recombination fractions. |
| genetic-mapping-functions | Genetic Mapping Functions |
| get_genomic_order | Get the genomic position of markers in a sequence |
| get_submap | Extract sub-map from map |
| get_tab_mrks | Get table of dosage combinations |
| group_mappoly | Assign markers to linkage groups |
| hexafake | Simulated autohexaploid dataset. |
| hexafake.geno.dist | Simulated autohexaploid dataset with genotype probabilities. |
| imf_h | Genetic Mapping Functions |
| imf_k | Genetic Mapping Functions |
| imf_m | Genetic Mapping Functions |
| 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 |
| loglike_hmm | Multipoint log-likelihood computation |
| make_mat_mappoly | Subset recombination fraction matrices |
| make_pairs_mappoly | Subset pairwise recombination fractions |
| make_seq_mappoly | Create a Sequence of Markers |
| maps.hexafake | Resulting maps from 'hexafake' |
| mds_mappoly | Estimates loci position using Multidimensional Scaling |
| merge_datasets | Merge datasets |
| merge_maps | Merge two maps |
| mf_h | Genetic Mapping Functions |
| mf_k | Genetic Mapping Functions |
| mf_m | Genetic Mapping Functions |
| plot.mappoly.data | Data Input |
| plot.mappoly.geno.ord | Get the genomic position of markers in a sequence |
| plot.mappoly.homoprob | Plots mappoly.homoprob |
| plot.mappoly.map | Multipoint analysis using Hidden Markov Models in autopolyploids |
| plot.mappoly.prefpair.profiles | Plots mappoly.prefpair.profiles |
| plot.mappoly.rf.matrix | Recombination fraction list to matrix |
| plot.mappoly.sequence | Create a Sequence of Markers |
| plot_genome_vs_map | Physical versus genetic distance |
| plot_GIC | Genotypic information content |
| plot_mappoly.map2 | Plot object mappoly.map2 |
| plot_map_list | Plot a genetic map |
| plot_mrk_info | Plot marker information |
| plot_progeny_dosage_change | Display genotypes imputed or changed by the HMM chain given a global genotypic error |
| print.mappoly.data | Data Input |
| print.mappoly.geno.ord | Get the genomic position of markers in a sequence |
| print.mappoly.map | Multipoint analysis using Hidden Markov Models in autopolyploids |
| print.mappoly.pcmap | Estimates loci position using Multidimensional Scaling |
| print.mappoly.pcmap3d | Estimates loci position using Multidimensional Scaling |
| print.mappoly.rf.matrix | Recombination fraction list to matrix |
| print.mappoly.sequence | Create a Sequence of Markers |
| print_mrk | Summary of a set of markers |
| 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 |
| segreg_poly | Polysomic segregation frequency |
| 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 |
| summary_maps | Summary maps |
| 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 approach and evaluating difference in LOD and gap size |
| update_map | Update map |