a5f1afbd80af65c0309d1e6c3178e445 *DESCRIPTION
303f0da3c928c52d049577b50bdb6044 *NAMESPACE
79e67799695f129899050c720ecad9af *R/aiding_functions.R
ce882c8f72ccf8aca2882331a44db1f8 *R/exported_functions.R
6d7df7870655acb3c185e80b9c0d9a69 *R/p4_functions.R
5756f992e2fe114e40522790f31e4806 *R/r2_functions.R
3859f1c996cff5d6b6d509be74c5900b *R/r3_functions.R
905cf32a6d446281f8b10ac4a16461de *R/r4_functions.R
b7d8ec75868c884e9e94fa1fd2c147fc *R/r6_functions.R
3ea6ed97adb1af447301aba310a43a01 *R/roxygen_datasets.R
121f4576a0451346129c7524c72414e0 *R/sysdata.rda
43455cd2f82819709f69d88115657cba *build/vignette.rds
2e017d9d11d73c2d111f37daf2f8edad *data/ALL_dosages.rda
875baa62048b4ccbe6d5d99ea36ce30c *data/LGHomDf_P1_1.rda
e24dd9040a6224689e156171e73221af *data/LGHomDf_P2_1.rda
bc2b898070ea9b3c2dfd022d1e1b4db0 *data/LGHomDf_P2_2.rda
2b9e0a408213367d989c172b9efff921 *data/P1_DxN_Assigned.rda
15625a42c51e8dd57cf41ed3d6b3e40c *data/P1_SxS_Assigned.rda
9ba2890b9d4048e6142a8a4e6b828f0d *data/P1_homologues.rda
63e5f703ef2143d265387af7102f8a05 *data/P2_DxN_Assigned.rda
e5701c0e7b79fd551a9710f0fbdcb655 *data/P2_SxS_Assigned.rda
10fffb7f2ac42ad90178dcc3bf500414 *data/P2_SxS_Assigned_2.rda
4445dba6501e0370e5134e114aa040cf *data/P2_homologues.rda
6717bf65655337d2ff80b98cac6a66ce *data/P2_homologues_triploid.rda
6f2715a7ffc12ee9f6f0b2b8d0471d57 *data/SN_DN_P1.rda
d1f42f2f9f75af802a075c8375fc5856 *data/SN_DN_P2.rda
11703e978786cd987e228935a29cb9e5 *data/SN_SN_P1.rda
09636c9fc774f291140da6df70eedb2f *data/SN_SN_P2.rda
d7d9f95e5de8d4ae4d702d3627055199 *data/SN_SN_P2_triploid.rda
fc799ad499ba92bb0f6c5a0fcca635ae *data/SN_SS_P1.rda
037f7276f2714b53d80214db43a71d32 *data/SN_SS_P2.rda
9f24c27fa151cccf6ce2cafaf4663cf2 *data/TRI_dosages.rda
dc12cb239ca9d96ea0ca94d70b05ab81 *data/all_linkages_list_P1.rda
859e3d330cc2f7cad6a15ba35897ba3d *data/all_linkages_list_P1_split.rda
7496708b80cfb9deb86476715c353b66 *data/all_linkages_list_P1_subset.rda
e9bc4e09cc88866ef56066ea09a6b529 *data/chk1.rda
158608afa441499e12bacf0de4697447 *data/exampleRAD_mapping.rda
516d3e7bedd2f19049f6852386c72c35 *data/gp_df.rda
b6f198a20e2edc9617b05ff38943a413 *data/integrated.maplist.rda
ea784fcddb6d2dccd6b52b513e6a49ff *data/map1.rda
4706a1758495cf78b502a716be54fe2e *data/map2.rda
73c1dc82a04f40cc5e866b369c2e96dd *data/map3.rda
9220f4224f57b497226c8660127350ad *data/maplist_P1.rda
3b66998e8763362209a42f0a7e586d15 *data/maplist_P1_subset.rda
d19e640b5214d2fc872f96c599f677b7 *data/maplist_P2_subset.rda
bb260483c6e915f9eff01fc56861245a *data/marker_assignments_P1.rda
fb1530bb1ee8232dc9c905870a139ffe *data/marker_assignments_P2.rda
7ec1ad14294808bb70905fcda8ffd4bd *data/mout.rda
a33afb837acde9f419fd029d2721cd61 *data/phased.maplist.rda
e42532fd70f97436f54ec370c60c20c6 *data/screened_data.rda
43ac32cfa93eecfe4a70f98e3a11ff82 *data/screened_data2.rda
8df63499b0b88f760be1ef610799c053 *data/screened_data3.rda
b2f9679c28f0792f5455a84baa0c4149 *data/segregating_data.rda
9965d6ff0ddbc8bcebc50dfaf96f7c05 *inst/doc/Vignette_genotype_probabilities.R
b7ae7dd8fe26cc42ff5c71213f450d1c *inst/doc/Vignette_genotype_probabilities.Rmd
947d624aada9ef9b43f91999b4287f94 *inst/doc/Vignette_genotype_probabilities.html
ffa06092aade0ad71717becd2ceb4c1a *inst/doc/Vignette_polymapR.R
3740ac59203a15daca81360492ef1f32 *inst/doc/Vignette_polymapR.Rmd
7fc65354951bb4bf89819270e459b987 *inst/doc/Vignette_polymapR.html
3e40662a7200976af6e9f3fe9a9f3a4b *man/ALL_dosages.Rd
8277578ddc23b54648a5bd4ea61fb955 *man/LGHomDf_P1_1.Rd
25d8d2b2c0ff77e4825c2b37b20d171a *man/MDSMap_from_list.Rd
c8f3faf8ed56be37b6ddf72363dc8fa1 *man/P1_SxS_Assigned.Rd
e9fc1d6ceed431a47a0952406c706102 *man/P1_homologues.Rd
9b82b18a98df9766a583d3b5a04bb11f *man/PCA_progeny.Rd
b01c6550843a4ddcbb50e3dffdca6e65 *man/SNSN_LOD_deviations.Rd
6669c0da3331f14a5718230b91d6bbda *man/SN_SN_P1.Rd
c7fb4c8bdd310d6112443b2d77954598 *man/add_dup_markers.Rd
c51b14c1e3aa438f945bf01e170bf0b0 *man/all_linkages_list_P1.Rd
19ca9e0f2c10f68115b24ed1f4aea7cd *man/assign_SN_SN.Rd
bdfcd6b1a03f6a09c96e9e2d3c379de1 *man/assign_linkage_group.Rd
e03e6769263b364ed5c4e24780ddbf8b *man/bridgeHomologues.Rd
7c2f16f595be1510c6de18f85619c464 *man/calcSegtypeInfo.Rd
aabe0b3f42529b2f1b489ca424a0daa1 *man/checkF1.Rd
f4b69b83a480d77e27bb0f64c9b50b27 *man/check_map.Rd
84d5de68f11d84501b10f8a73d3246a9 *man/check_marker_assignment.Rd
9afac2ea9c9e64fcb04b35da9f3316f0 *man/check_maxP.Rd
b87bb3e040c16cdcc821b93cc85cc2e9 *man/chk1.Rd
c1ee00c088dabe1c9fb925e70be4eb23 *man/cluster_SN_markers.Rd
7e33c5b774f4771e0c59ebcf83d9eca7 *man/cluster_per_LG.Rd
7b1d920eefff9e105529dd06a0c5dd2d *man/compare_maps.Rd
ffe144096e890ae4d891945475704897 *man/consensus_LG_assignment.Rd
fae4fe58b4dbef5dd3fdeaed6bbd393c *man/consensus_LG_names.Rd
788f21ab3b348a43da0eff0673f79b3e *man/convert_marker_dosages.Rd
4519fad8e721b2e601d729bb86c1e60e *man/convert_polyRAD.Rd
749e742e47634998fd1629804ce76b3b *man/convert_updog.Rd
597ae8deb7e224a6bf2880e94210aa8d *man/correctDosages.Rd
76a5adf3d8f710e44d9ccac3bf290ab0 *man/createTetraOriginInput.Rd
7e9113a21966e8b440cc19bbc8666038 *man/create_phased_maplist.Rd
459911929a7886305c34992a130fbd09 *man/define_LG_structure.Rd
991f49c096925678a368bdbfb74c8d70 *man/exampleRAD_mapping.Rd
e749e5d2f1d0bff8ae57f07e4b1633c0 *man/finish_linkage_analysis.Rd
963b09a7e0e1ab7d5b12ce38ddb07129 *man/get_markertype_combinations.Rd
f8852ea755f4b809ab9e155fdf214439 *man/gp_df.Rd
c5a3bb830a24b7c5d1a678ef2b7d88d0 *man/gp_overview.Rd
3d0ca175ffaa1b368bc3490e8b948304 *man/homologue_lg_assignment.Rd
9bd3ed74dd1a5a5c02881d203d547564 *man/integrated.maplist.Rd
0ae2bd9c3bab4c066c9bece9578cea0f *man/linkage.Rd
bb64f98a74bd716497f021f7fee8c4a9 *man/linkage.gp.Rd
a7c8959978e20fdd7c9dbd44464afc7f *man/map1.Rd
bc0229f1e03410731a8ad5c5fb584ef5 *man/map2.Rd
93eb6c96bc6357b722fe4756b8dd4573 *man/map3.Rd
c6432fab1d5429c23fd253a4858921e8 *man/maplist_P1.Rd
a37da6a7aed2e5b6344c7d9c7f55e1ef *man/marker_binning.Rd
58a7e44b0d543bd40a99b29c1195f8e6 *man/marker_data_summary.Rd
f8cc4b4b5a48a33a0b689e4d26b02642 *man/merge_homologues.Rd
b17c738e378b2f7ad810b6c33137013e *man/merge_marker_assignments.Rd
72bc16360d7fbb459d856df9085c811e *man/mout.Rd
7d55350b77e8fcb539b178eeec093646 *man/overviewSNlinks.Rd
23e81cbcee3511e80313a7ebf7067754 *man/p4_functions.Rd
a65775d971e1463b80a6cf2002569ec5 *man/parental_quantities.Rd
0b49ce4a9c774524e42a3828ff7633a0 *man/phase_SN_diploid.Rd
512abeb454fa0b5d1219e77fcb2ae498 *man/phased.maplist.Rd
6abaa841273b083f70f5375e8592ba57 *man/plot_hom_vs_LG.Rd
44279614bf195e0ecd6231c921bcb375 *man/plot_linkage_df.Rd
ada84b31433d355c87fa97d419d83f87 *man/plot_map.Rd
df097a7e61d993a7fcd552d9a8edaea9 *man/plot_phased_maplist.Rd
b8ed2165fb93d7618d1a3bb541eb059e *man/polymapR.Rd
3de384bf3cda08c8d70e83b50212618a *man/r2_functions.Rd
6137b98ade768768b63e6afc11f93b37 *man/r3_functions.Rd
06be89ac35f2a24b7d8836336b2f640b *man/r4_functions.Rd
b196bfe0083727bd8ae6c8913a49a0a2 *man/r6_functions.Rd
5b536c5098e1b391d1b62d70c3e89669 *man/r_LOD_plot.Rd
1bfd9b7436c1692aabdf16f65e185361 *man/screen_for_NA_values.Rd
7132bdfa9d921c14895e9472a3e878b3 *man/screen_for_duplicate_individuals.Rd
389a734639f0d0dc38fea74d81668427 *man/screen_for_duplicate_individuals.gp.Rd
1e3a374f2349a5a8b00e1cf2b4e168c0 *man/screen_for_duplicate_markers.Rd
7be606048955f644f330b55f3c3a0663 *man/test_prefpairing.Rd
b1e9d773ad64f1b29ffd9ddc8e4b1246 *man/write.TSNPM.Rd
35a7027ace86217619389e3d7b275b1a *man/write.mct.Rd
a9d987c8e2786ece522553bb640a8fc0 *man/write.pwd.Rd
2a60e42fd8d8544f7940b9581628bc20 *man/write_nested_list.Rd
84937cc1d4fe8254ef1a8d59d352a755 *man/write_pwd_list.Rd
b7ae7dd8fe26cc42ff5c71213f450d1c *vignettes/Vignette_genotype_probabilities.Rmd
3740ac59203a15daca81360492ef1f32 *vignettes/Vignette_polymapR.Rmd
4d8542934ab9dce5dce5f4d204c29f4b *vignettes/bibliography.bib
2a525a4d0bfde9865b47c532ce586782 *vignettes/biomed-central.csl
5dc658364062570363f2d3e716151347 *vignettes/data
a5fd82de83b40774bd0ca26515efe899 *vignettes/figures/LG1_check_map_plotA.png
a1115d015d3392b1c5fd9a307d305477 *vignettes/figures/LG1_check_map_plotB.png
62117229351313b470e892395319ab45 *vignettes/figures/P1_bridges.png
74174c3d6144b73b9c7ee7ea1d7566d0 *vignettes/figures/P2_bridges.png
c56c6fb5245ee6c2097a56cba6da586c *vignettes/figures/cluster_per_LG_P1.3.png
4d56a44042f27741a7a09bd8519af40a *vignettes/figures/dup_indivs.png
fd6b268afeacdc07e973e79e4628d155 *vignettes/figures/gp_overview.png
aee4e74ba418da7d79366f48d2af7eac *vignettes/figures/maxPdist.png
3bd61490eb47776b4e3f6b13b01c9b18 *vignettes/figures/meiosis_4x.png
242c27adf716ebdbbebaa72e273490a2 *vignettes/figures/p1_clustering_gp.png
90c5360f78726c6248bbe0e0b30d1488 *vignettes/figures/p2_clustering_gp.png
953b6779efefe173f5aad794190968ac *vignettes/genoprobsdata.RData
d8f753b0f7c1856fe4a80d206dfa1b97 *vignettes/polymapR_vignette.RData
