R/utils.R
R/est_map_hmm.R
R/pairwise_rf.R
R/read_mappoly.R
R/check_phase_configurations.R
R/filters.R
R/read_mappoly_vcf.R
R/haplotype_map_utils.R
R/preferential_pairing.R
R/make_seq.R
R/read_fitpoly.R
R/read_mappoly_prob.R
R/import_from_polymapR.R
R/merge_maps.R
R/get_counts.R
R/rf_list_to_matrix.R
R/mds.R
R/marker_info.R
R/calc_genoprob.R
R/simulation_utils.R
R/reestimate_map_with_global_genotypic_error.R
R/read_mappoly_csv.R
R/group.R
R/calc_genoprob_error.R
R/get_submap.R
R/cache_twopts.R
R/homolog_probs.R
R/import_from_updog.R
R/calc_genoprob_dist.R
R/plot_map_list.R
R/reestimate_map.R
R/reestimate_map_with_prior_genotypic_probability.R
R/split_and_rephase.R
R/one_paprent_single_map_hmm.R
R/calc_genoprob_one_parent.R
R/single_map_hmm.R
R/plot_genome_vs_map.R
R/sim_homologous.R
R/export_map_list.R
R/poly_cross_simulate.R
R/rf_snp_filter.R
R/eliminate_redundant.R
R/get_counts_from_web.R
R/loglike_hmm.R
R/prior_dist_hmm.R
R/make_mat.R
R/make_pairs.R
R/segreg_poly.R
R/zzz.R
src/pairwise_estimation.cpp
src/est_hmm_map_based_on_phased_mrk_blocks.cpp
src/est_map_hmm_given_prior.cpp
src/est_map_hmm_given_dose.cpp
src/hmm_one_parent.cpp
src/hmm_elements.cpp
src/read_mappoly_vcf.cpp
src/calc_genoprob_based_on_phased_marker_blocks.cpp
src/combinatorial.cpp
src/calc_genoprob.cpp
src/calc_loglike_given_map.cpp
src/genotypic_counts.cpp
src/mappoly_init.c