Files in mappoly
Genetic Linkage Maps in Autopolyploids
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/read_mappoly.R
R/RcppExports.R
R/find_blocks.R
R/sysdata.rda
R/reestimate_map.R
R/get_submap.R
R/export_map_list.R
R/loglike_hmm.R
R/plot_genome_vs_map.R
R/single_map_hmm.R
R/calc_genoprob_one_parent.R
R/marker_info.R
R/segreg_poly.R
R/read_mappoly_vcf.R
R/make_mat.R
R/poly_cross_simulate.R
R/group.R
R/filters.R
R/calc_genoprob.R
R/data.R
R/get_counts.R
R/reest_map_error.R
R/read_mappoly_csv.R
R/simulation_utils.R
R/export_qtlpoly.R
R/check_phase_configurations.R
R/calc_genoprob_error.R
R/make_pairs.R
R/est_map_hmm.R
R/import_from_polymapR.R
R/one_paprent_single_map_hmm.R
R/cache_twopts.R
R/pairwise_rf.R
R/homolog_probs.R
R/split_and_rephase.R
R/rf_list_to_matrix.R
R/import_from_updog.R
R/get_counts_from_web.R
R/calc_genoprob_dist.R
R/merge_maps.R
R/read_fitpoly.R
R/make_seq.R
R/plot_map_list.R
R/mds.R
R/zzz.R
R/prior_dist_hmm.R
R/sim_homologous.R
R/haplotype_map_utils.R
R/preferential_pairing.R
R/read_mappoly_prob.R
R/eliminate_redundant.R
R/utils.R
src/Makevars.win
src/calc_loglike_given_map.cpp
src/hmm_elements.cpp
src/est_map_hmm_given_prior.cpp
src/combinatorial.h
src/RcppExports.cpp
src/calc_loglike_given_map.h
src/calc_genoprob.cpp
src/pairwise_estimation.cpp
src/genotypic_counts.cpp
src/calc_genoprob.h
src/est_map_hmm_given_dose.cpp
src/read_mappoly_vcf.cpp
src/combinatorial.cpp
src/est_hmm_map_based_on_phased_mrk_blocks.cpp
src/mappoly_init.c
src/est_hmm_map_based_on_phased_mrk_blocks.h
src/calc_genoprob_based_on_phased_marker_blocks.cpp
src/est_map_hmm_given_prior.h
src/pairwise_estimation_rcppparallel.cpp
src/hmm_one_parent.cpp
src/hmm_elements.h
src/genotypic_counts.h
src/est_map_hmm_given_dose.h
src/calc_genoprob_based_on_phased_marker_blocks.h
inst/CITATION
inst/doc/mappoly_startguide.html
inst/doc/mappoly_startguide.Rmd
inst/doc/mappoly_startguide.R
inst/extdata/potato_example.csv
build/vignette.rds
build/partial.rdb
tests/testthat.R
tests/testthat/test-reestmap.R
tests/testthat/test-utility_func.R
tests/testthat/test-read_data.R
tests/testthat/test-calc_genoprobs.R
tests/testthat/test-merge_maps.R
tests/testthat/test-filters.R
tests/testthat/test-split_and_rephase.R
tests/testthat/test-preferential_pairing.R
tests/testthat/test-est_hmm_map.R
tests/testthat/test-est_with_probs.R
tests/testthat/test-homolog_prob.R
tests/testthat/test-group.R
tests/testthat/test-simulation.R
tests/testthat/test-2pt.R
tests/testthat/test-get_submap.R
tests/testthat/test-export_map_list.R
vignettes/mappoly_startguide.Rmd
vignettes/images/fig10.jpeg
vignettes/images/fig11.jpeg
vignettes/images/fig6.jpeg
vignettes/images/fig2.jpeg
vignettes/images/fig3.jpeg
vignettes/images/fig1.jpeg
vignettes/images/fig5.jpeg
vignettes/images/fig8.jpeg
vignettes/images/fig7.jpeg
vignettes/images/fig9.jpeg
vignettes/images/fig4.jpeg
data/datalist
data/example_data.rda
man/est_rf_hmm_sequential.Rd
man/maps.hexafake.Rd
man/sample_data.Rd
man/parallel_block.Rd
man/reest_rf.Rd
man/mf_k.Rd
man/get_counts_two_parents.Rd
man/mrk_chisq_test.Rd
man/get_LOD.Rd
man/msg.Rd
man/sim_homologous.Rd
man/print_ph.Rd
man/calc_genoprob_one_parent.Rd
man/get_genomic_order.Rd
man/calc_homologprob.Rd
man/est_pairwise_rf.Rd
man/filter_individuals.Rd
man/est_pairwise_rf2.Rd
man/solcap.mds.map.Rd
man/segreg_poly.Rd
man/paralell_pairwise_probability.Rd
man/imf_k.Rd
man/get_full_info_tail.Rd
man/paralell_pairwise_discrete_rcpp.Rd
man/get_states_and_emission_one_parent.Rd
man/drop_marker.Rd
man/filter_non_conforming_classes.Rd
man/ph_matrix_to_list.Rd
man/filter_missing.Rd
man/paralell_pairwise_discrete.Rd
man/aggregate_matrix.Rd
man/concatenate_new_marker.Rd
man/find_blocks.Rd
man/imf_m.Rd
man/export_map_list.Rd
man/make_pairs_mappoly.Rd
man/solcap.err.map.Rd
man/plot_genome_vs_map.Rd
man/imf_h.Rd
man/sim_cross_one_informative_parent.Rd
man/plot_GIC.Rd
man/get_ph_list_subset.Rd
man/compare_maps.Rd
man/solcap.prior.map.Rd
man/read_geno.Rd
man/add_marker.Rd
man/est_rf_hmm.Rd
man/read_geno_prob.Rd
man/est_rf_hmm_single_one_parent.Rd
man/check_ls_phase.Rd
man/merge_maps.Rd
man/import_data_from_polymapR.Rd
man/rf_list_to_matrix.Rd
man/est_full_hmm_with_prior_prob.Rd
man/table_to_mappoly.Rd
man/calc_genoprob.Rd
man/compare_haplotypes.Rd
man/make_mat_mappoly.Rd
man/perm_tot.Rd
man/get_w_m.Rd
man/sim_cross_two_informative_parents.Rd
man/is.prob.data.Rd
man/plot_one_map.Rd
man/extract_map.Rd
man/plot_compare_haplotypes.Rd
man/get_ph_conf_ret_sh.Rd
man/elim_redundant.Rd
man/get_dosage_type.Rd
man/filter_missing_ind.Rd
man/split_mappoly.Rd
man/filter_segregation.Rd
man/generate_all_link_phases_elim_equivalent_haplo.Rd
man/plot.mappoly.homoprob.Rd
man/create_map.Rd
man/make_seq_mappoly.Rd
man/filter_map_at_hmm_thres.Rd
man/poly_cross_simulate.Rd
man/plot.mappoly.prefpair.profiles.Rd
man/genotyping_global_error.Rd
man/read_vcf.Rd
man/check_data_sanity.Rd
man/calc_genoprob_error.Rd
man/read_geno_csv.Rd
man/est_full_hmm_with_global_error.Rd
man/mp_pallet2.Rd
man/mp_pallet3.Rd
man/plot_mrk_info.Rd
man/perm_pars.Rd
man/draw_phases.Rd
man/check_data_dose_sanity.Rd
man/draw_cross.Rd
man/get_cache_two_pts_from_web.Rd
man/concatenate_ph_list.Rd
man/select_rf.Rd
man/plot_map_list.Rd
man/print_mrk.Rd
man/gg_color_hue.Rd
man/import_from_updog.Rd
man/hexafake.Rd
man/est_haplo_hmm.Rd
man/update_ph_list_at_hmm_thres.Rd
man/calc_prefpair_profiles.Rd
man/mf_m.Rd
man/get_ij.Rd
man/est_rf_hmm_single.Rd
man/get_indices_from_selected_phases.Rd
man/get_tab_mrks.Rd
man/v_2_m.Rd
man/tetra.solcap.geno.dist.Rd
man/est_map_haplo_given_genoprob.Rd
man/cache_counts_twopt.Rd
man/check_if_rf_is_possible.Rd
man/prepare_map.Rd
man/dist_prob_to_class.Rd
man/summary_maps.Rd
man/export_qtlpoly.Rd
man/get_rf_from_list.Rd
man/update_missing.Rd
man/mf_h.Rd
man/get_rf_from_mat.Rd
man/hexafake.geno.dist.Rd
man/calc_genoprob_haplo.Rd
man/get_counts.Rd
man/ls_linkage_phases.Rd
man/group_mappoly.Rd
man/mp_pallet1.Rd
man/elim_conf_using_two_pts.Rd
man/update_map.Rd
man/get_submap.Rd
man/import_phased_maplist_from_polymapR.Rd
man/get_counts_all_phases.Rd
man/calc_genoprob_dist.Rd
man/get_counts_one_parent.Rd
man/ph_list_to_matrix.Rd
man/generate_all_link_phase_elim_equivalent.Rd
man/poly_hmm_est.Rd
man/check_pairwise.Rd
man/cat_phase.Rd
man/loglike_hmm.Rd
man/elim_equiv.Rd
man/rev_map.Rd
man/format_rf.Rd
man/filter_missing_mrk.Rd
man/split_and_rephase.Rd
man/get_ols_map.Rd
man/export_data_to_polymapR.Rd
man/read_fitpoly.Rd
man/add_mrk_at_tail_ph_list.Rd
man/rf_snp_filter.Rd
man/tetra.solcap.Rd
man/solcap.dose.map.Rd
man/merge_datasets.Rd
man/mds_mappoly.Rd
man/check_data_dist_sanity.Rd
