Files in mmollina/polymap
Construction of Genetic Linkage Maps in Autopolyploids

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DESCRIPTION
LICENSE
NAMESPACE
R/cache_twopts.R R/calc_genoprob.R R/check_phase_configurations.R R/data.R R/drop_mrk.R R/eliminate_redundant.R R/est_map_hmm.R R/get_counts.R R/get_counts_from_web.R R/group.R R/make_mat_polymap.R R/make_pairs_polymap.R R/make_seq.R R/mds.R R/pairwise_rf.R R/poly_cross_simulate.R R/read_polymap.R R/reestimate_map.R R/rf_list_to_matrix.R R/rf_snp_filter.R R/segreg_poly.R R/sim_homologous.R R/simulation_utils.R R/single_map_hmm.R R/utils.R README.Rmd README.md
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TODOs
data/hexafake.RData
inst/doc/final_pipeline.R
inst/doc/phase_sim_hexa_P.csv
inst/doc/phase_sim_hexa_Q.csv
inst/doc/rf1.cvs
inst/doc/rf2.cvs
inst/doc/rf3.cvs
inst/extdata/hexafake
man/cache_counts_twopt.Rd man/calc_genoprob.Rd man/calc_maps_load_and_trim_prin_curve.Rd man/calc_nnfit.Rd man/calc_nnfit_loci.Rd man/check_pairwise.Rd man/compare_haplotypes.Rd man/concatenate_new_marker.Rd man/create_map.Rd man/draw_alleles.Rd man/draw_cross.Rd man/draw_homologous.Rd man/draw_phases.Rd man/drop_mrk.Rd man/elim_conf_using_two_pts.Rd man/elim_equiv.Rd man/elim_redundant.Rd man/est_pairwise_rf.Rd man/est_rf_hmm.Rd man/est_rf_hmm_sequential.Rd man/est_rf_hmm_single.Rd man/format_rf.Rd man/generate_all_link_phase_elim_equivalent.Rd man/get_LOD.Rd man/get_cache_two_pts_from_web.Rd man/get_counts.Rd man/get_counts_all_phases.Rd man/get_counts_one_parent.Rd man/get_counts_two_parents.Rd man/get_dist_loci.Rd man/get_full_info_tail.Rd man/get_ij.Rd man/get_indices_from_selected_phases.Rd man/get_nearest_informative.Rd man/get_ph_conf_ret_sh.Rd man/get_rf_from_list.Rd man/get_rf_from_mat.Rd man/get_submap.Rd man/group_polymap.Rd man/hexafake.Rd man/imf_h.Rd man/imf_k.Rd man/imf_m.Rd man/ls_linkage_phases.Rd man/make_mat_polymap.Rd man/make_pairs_polymap.Rd man/make_seq_polymap.Rd man/mds_polymap.Rd man/mean_dist_from_truth.Rd man/mf_h.Rd man/mf_k.Rd man/mf_m.Rd man/paralell_pairwise.Rd man/perm_pars.Rd man/perm_tot.Rd man/ph_list_to_matrix.Rd man/ph_matrix_to_list.Rd man/plot_compare_haplotypes.Rd man/plot_diag_pc.Rd man/plot_diag_pc_3d.Rd man/poly_cross_simulate.Rd man/pos_twopt_est.Rd man/print.polymap.group.Rd man/print_mrk.Rd man/read_geno.Rd man/recalc_nnfit_from_map.Rd man/reest_map.Rd man/rf_list_to_matrix.Rd man/rf_snp_filter.Rd man/segreg_poly.Rd man/select_rf.Rd man/sim_cross_one_informative_parent.Rd man/sim_cross_two_informative_parents.Rd man/sim_homologous.Rd
polymap.Rproj
src/calc_genoprob.cpp
src/calc_genoprob.h
src/combinatorial.cpp
src/combinatorial.h
src/est_map_hmm_given_dose.cpp
src/est_map_hmm_given_dose.h
src/genotypic_counts.cpp
src/genotypic_counts.h
src/hmm_elements.cpp
src/hmm_elements.h
src/pairwise_estimation.cpp
src/pairwise_estimation.h
src/polymap_init.c
mmollina/polymap documentation built on Jan. 14, 2018, 10:49 p.m.