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.
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
plot.mappoly.homoprob   Plots mappoly.homoprob
plot.mappoly.prefpair.profiles
                        Plots mappoly.prefpair.profiles
plot_GIC                Genotypic information content
plot_genome_vs_map      Physical versus genetic distance
plot_map_list           Plot a genetic map
plot_mappoly.map2       Plot object mappoly.map2
plot_mrk_info           Plot marker information
plot_progeny_dosage_change
                        Plot progeny dosage changes after HMM-based
                        correction with a global error model
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
