# Genetic Linkage Maps in Autopolyploids

## Documentation for package ‘mappoly’ version 0.4.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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 | Plot progeny dosage changes after HMM-based correction with a global error model
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
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