# Genetic Linkage Maps in Autopolyploids

## Documentation for package ‘mappoly’ version 0.3.3

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

## 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_one_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
drop_marker | Remove markers from a map
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_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
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.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_map_list | Plot a genetic map
plot_mrk_info | Plot marker information
poly_cross_simulate | Simulate an autopolyploid full-sib population
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_map | Update map
update_missing | Update missing information