Man pages for mmollina/polymap
Construction of Genetic Linkage Maps in Autopolyploids

cache_counts_twoptFrequency of genotypes for two-point estimaton of...
calc_genoprobCompute QTL conditional probability
calc_genoprob_distCompute the conditional QTL probabilities using genotype...
calc_maps_load_and_trim_prin_curveEstimates loci position using Principal curves
calc_nnfitcalc nnfit
calc_nnfit_lociGet nearest informative marker
check_pairwiseCheck if all pairwise combinations of elements of 'input.seq'...
compare_haplotypesCompare two polyploid haplotypes stored in list format
concatenate_new_markerInsert a new marker at the end of the sequence taking into...
create_mapCreate a marker with pseudomarkers
dist_prob_to_classSelects the class with high probability and return it instead...
draw_allelesdraw alleles
draw_crossDraw simple parental linkage phase configurations
draw_homologousdraw homologous
draw_phasesPlot the linkage phase configuration given a list of...
drop_mrkDrop markers in a genetic map
elim_conf_using_two_ptsEliminate unlikely configuration phases given the two-point...
elim_equivDrop equivalent linkage phase configurations, i.e. the ones...
elim_redundantEliminate redundant markers
est_pairwise_rfPairwise two-point analysis
est_rf_hmmMultipoint analysis using Hidden Markov Models in...
est_rf_hmm_sequentialMultipoint analysis using Hidden Markov Models - Sequential...
est_rf_hmm_singleMultipoint analysis using Hidden Markov Models (single phase)
format_rfFormat results from pairwise two-point estimation in C++
generate_all_link_phase_elim_equivalentGenerate all possible linkage phases in matrix form given the...
get_cache_two_pts_from_webAccess a remote server to get Counts for recombinat classes
get_countsCounts for recombinat classes
get_counts_all_phasesCounts for recombinat classes
get_counts_one_parentCounts for recombinat classes in a polyploid parent.
get_counts_two_parentsCounts for recombinat classes
get_dist_lociget_dist_loci
get_full_info_tailGet the tail of a marker sequence up to the point where the...
get_ijGiven a pair of character indicating the numbers i and j :...
get_indices_from_selected_phasesGet the indices of selected linkage phases given a threshold
get_LODExtract the LOD Scores in a "polymap.compare" or...
get_nearest_informativeGet nearest informative marker
get_ph_conf_ret_shGiven a homology group in matrix form, it returns the number...
get_rf_from_listGet the recombination fraction for a sewquence of markers...
get_rf_from_matGet recombination fraction from a matrix
get_submapExtract sub-map from map
group_polymapAssign markers to linkage groups
hexafakeSimulated autohexaploid dataset.
imf_hMap functions
imf_kMap functions
imf_mMap functions
ls_linkage_phasesList of linkage phases
make_mat_polymapSubset recombination fraction matrices
make_pairs_polymapSubset pairwise recombination fractions
make_seq_polymapCreate a sequence of markers
mds_polymapEstimates loci position using Multidimensional Scaling
mean_dist_from_truthCalculates the mean of the square distances of points from...
mf_hMap functions
mf_kMap functions
mf_mMap functions
paralell_pairwiseWrapper function to pairwise two-point estimation in C++
perm_parsN!/2 combination
perm_totN! combination
ph_list_to_matrixThis function converts linkage phase configurations from list...
ph_matrix_to_listThis function converts linkage phase configurations from...
plot_compare_haplotypesPlot two overlapped haplotypes
plot_diag_pcPlot disgnostic graphics (2D)
plot_diag_pc_3dPlot disgnostic graphics (3D)
poly_cross_simulateSimulate an autopolyploid full-sib population
poly_hmm_estEstimate genetic map using as input the probability...
pos_twopt_estCheck if it is possible to estimate the recombination...
print_mrkSummary of a set of markers
read_genoData Input
read_geno_distData Input
recalc_nnfit_from_mapCalculates a new nnfit based on a new order after estimating...
reest_mapReestimate the recombination fractions in a genetic map
reest_map_geno_distReestimate map using genotype distribution
rev_mapReverse map
rf_list_to_matrixRecombination fraction list to matrix
rf_snp_filterRemove snps that do not meet a LOD criteria
segreg_polyPolysomic segregation frequency
select_rfSelect rf adn lod based on thresholds
sim_cross_one_informative_parentSimulate mapping population (one parent)
sim_cross_two_informative_parentsSimulate mapping population (tow parents)
sim_homologousSimulate homology groups
mmollina/polymap documentation built on May 15, 2018, 7:21 p.m.