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604962522e7dfee6a23debf529295a7d *DESCRIPTION
753c7ba259fd7b8394cc421eac49350d *NAMESPACE
d9b39f1033092f123dba7ed8cce21e86 *R/aiding_functions.R
4c3af5e20028853bbe936d7ecc2abb3b *R/exported_functions.R
f7debfeee997ee9e3ae7023fe513c363 *R/p4_functions.R
b5c169256a6ec4bc76b1c74ff3705d49 *R/r3_functions.R
9f52171e188699863bae9d8e2807cdf2 *R/r4_functions.R
509041802ccb80a39e67dec24a6670b1 *R/r6_functions.R
71f27b563c67dce6b0279c5a2064fa19 *R/roxygen_datasets.R
a2a8c40dd247fc8dd8334c5181308800 *R/sysdata.rda
5129be0d3541c42bbb75dcc0596cce58 *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
03a5972b9f6777e3b6848d18f154a01d *data/datalist
b6f198a20e2edc9617b05ff38943a413 *data/integrated.maplist.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
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
cb5a3c651c3876d0a8a1a3c633135bc5 *inst/doc/Vignette_polymapR.R
01a47d7864d0dc34075ed58a1428fe6c *inst/doc/Vignette_polymapR.Rmd
9cd8c25f2bfaf941e77565c1cbc66c5e *inst/doc/Vignette_polymapR.html
4d5f4f9b98c18a2406c903f9fe0adb01 *man/ALL_dosages.Rd
37a29f084f1bcba21b886edb7c8b037f *man/LGHomDf_P1_1.Rd
36daf0be6f51f266a69faa9e419a3f99 *man/MDSMap_from_list.Rd
a07d3a9ae6d9c464edc9a0cd6df2a7c1 *man/Mode.Rd
5837e97fef14551a3e0d55102c63b997 *man/P1_SxS_Assigned.Rd
c0be7e3e00cfe60a7ff87da080ac6379 *man/P1_homologues.Rd
3af615e99581a4db4359ab279bda0079 *man/PCA_progeny.Rd
bea2f10481ba421e6a201f5919fa4645 *man/SNSN_LOD_deviations.Rd
fc33f1e9af3b292f86e1fc1f759ae5d9 *man/SN_SN_P1.Rd
f8b2e16329dc55673f56d5b3df292fed *man/add_dup_markers.Rd
eac827267103477669ef2648828b14fe *man/all_linkages_list_P1.Rd
d3300843952ba9b22471deeb0044e2c1 *man/assign_SN_SN.Rd
073c3c3dbffc38af93d3297564b60e25 *man/assign_linkage_group.Rd
3a3fc91ea3a8564f96505dbb7c79e2ad *man/bridgeHomologues.Rd
4d3f1fe20e0111d23dbd1556ba3c746a *man/calcPotShifts.Rd
0ec5058e2dd05889ca000f13e7a58474 *man/calcSegtypeInfo.Rd
4ddf3669ec671ec54950550b70b0ff6a *man/calc_binning_thresholds.Rd
6e1c7cd96d883cb2104b2636c22c5e3b *man/calc_q1.Rd
5490ad8fc7fa97bbfccc2d8d478ed03e *man/calc_q2.Rd
4abebe6cf29e46fad81c042f11a69839 *man/calc_q3.Rd
918109c89e948901e39cfec8e61f30a2 *man/calc_qall.Rd
0758f79220a02ae5a7a78cbe0a8913fd *man/checkF1.Rd
d80c1da9b9ffd777630af63e713da279 *man/checkFilename.Rd
51249400bf2136dfff3649e1c81b4ce1 *man/check_map.Rd
dd0ab56b21ba6bada86d1f2a270d4f14 *man/check_marker_assignment.Rd
177655396a5200a17c2caf7a5fa2c5af *man/chk2integer.Rd
1265615555cc5b25b0f1585559c85d31 *man/cluster_SN_markers.Rd
bfadede26a469ab3f8110b52e8e5ef2a *man/cluster_per_LG.Rd
45610946ad478581f081cffcd38bd29f *man/colour.bar.Rd
005e339e3b1854c1a796c3bacf6aa0da *man/consensus_LG_assignment.Rd
29e06787bec64b752653f1f82573fad1 *man/consensus_LG_names.Rd
eed987ae6e981bdf5ca8ce3e1b964f3e *man/convert_marker_dosages.Rd
3971d9398f267d1d18cf7e4257d82c78 *man/correctDosages.Rd
8092cd797389aacbdd969a9eb65a9e9c *man/createChmHomList.Rd
647c80078c574a65647b73eb9c162b81 *man/createMap.Rd
2a3303cbe62908be0e323f32f6bba854 *man/createTetraOriginInput.Rd
2ea7823807f2566dff4e38bb8435dcf8 *man/create_phased_maplist.Rd
1dccaaefa95c97423128c2fd34c29165 *man/define_LG_structure.Rd
2e0ba6ca33860fc1c92fede6be739351 *man/digamfrq.Rd
c9c2a21a07bd55acface0935230b6040 *man/finish_linkage_analysis.Rd
e8c280ac8b7dab3d21a98c59dcb527c4 *man/gcd.Rd
593e4c4e9eeb879b9da02b1299cdb9aa *man/gcd_all.Rd
6518d93211e282c31f3c85debc61f2b4 *man/getConsensusGeno.Rd
00659a27585c7aa2eba853534cc97121 *man/getMatchParents.Rd
86b7d2f6567254bcab00672faf835781 *man/get_markertype_combinations.Rd
edfa3cfb9012041a39508ef64a607954 *man/homologue_lg_assignment.Rd
b1ef02e2a162470440b48fd5301a8c5a *man/integrated.maplist.Rd
f1e9e09f57ce5f329bef63b722f96e09 *man/leftstr.Rd
7190ba02540b4799a4ec4f4c4757a855 *man/linkage.Rd
90962aab004a6232f37055f290c9868f *man/linterpol.Rd
af912027eef74ef596789df7070f2a0c *man/makeProgeny.Rd
1107052bf0fdaba60c94102d34fb0aae *man/maplist_P1.Rd
5a0f21dbab0dcd1cf127e51cbcbf2d9b *man/marker_binning.Rd
400eaedbef96e86eaafb9ee41a17704e *man/marker_binning_list.Rd
415a922810888402916d321134685361 *man/marker_data_summary.Rd
8d7b2aca3e93a3afa01dd416328e5a6c *man/merge_homologues.Rd
02881cd3a54dbd74280509836bc46c64 *man/merge_marker_assignments.Rd
dcd199b75251f9ea0bcb6aca481c2d28 *man/orient_and_merge_maps.Rd
e9d2ad87ae4a07ea5cb2870e90268714 *man/overviewSNlinks.Rd
2b8ee491e62dd4ddadb8ff306d811b85 *man/p4_functions.Rd
8bf95a2812dcf07dd06a2eac73c64569 *man/parental_quantities.Rd
c09075bb36dd11a4ba96441fdda04c1d *man/phase_SN_diploid.Rd
b63c5e61828c3ce47f0f5b8e47f094df *man/phased.maplist.Rd
ae10446fbff58bcb5333dd975bd73f30 *man/plot_SNlinks.Rd
9e2f4d4cb446635b7054285c4747469a *man/plot_hom_vs_LG.Rd
d085b2754579670014ae1877c7c41433 *man/plot_linkage_df.Rd
ab077a13a2a696722049fde4636b6ae3 *man/plot_map.Rd
1158e329e03f4834da1f91b266d542af *man/plot_phased_maplist.Rd
ace24074c007224333918da558a14a9a *man/polygamfrq.Rd
a0a67fc4f245abb87e5a016483a32bf7 *man/polymapR.Rd
7b7c305c2d88c181cecd412a2f477756 *man/prepare_pwd.Rd
2dd4f0a659f2b94120c51feca5fe3f59 *man/r3_functions.Rd
d7b4117e6a69b9c5dc06d4779000c4e9 *man/r4_functions.Rd
e8dc9cf1dc747d4f5c82ee6dd1e3bd7c *man/r6_functions.Rd
d4478db1045ea256d8806b97b5d5aa01 *man/r_LOD_plot.Rd
69de6542b582cba2a408c86b94d3073d *man/rightstr.Rd
b59bec0c986bed7f94fe44ffff4bc250 *man/screen_for_NA_values.Rd
8a9fe85b283c3e428e7cfb4314b20e8f *man/screen_for_duplicate_individuals.Rd
ae3a350a7482f889aab7dfb1c156b01c *man/screen_for_duplicate_markers.Rd
83f9355cb2f13f772f3d9656d8e49778 *man/segtypeInfoSummary.Rd
f7b7396cccf16bd0724c6c4c8f96b29e *man/selSegtypeInfo.Rd
f5a5f09e5ae185b8c1f7e8a03d061f45 *man/split_linkage_info.Rd
c157bf5c32d2e7a4b8d54f7b4b926bda *man/test_LG_hom_stack.Rd
35eb1766eb72e08df8ada6dd045462f0 *man/test_cluster_stack.Rd
1ad610753fd2fb406499e7657e50bdfb *man/test_dosage_matrix.Rd
da573a012b9befe7c8dd0f83e1665c05 *man/test_linkage_df.Rd
323c6bcdab5f90f83cd5920b7062fce7 *man/test_prefpairing.Rd
3d6a9c182454ed765d542358d401cc4c *man/vector.to.matrix.Rd
30523aed8fa91e64c7752e0415cf8bc6 *man/write.TSNPM.Rd
1db437e618a766a2a8d2878717881313 *man/write.logheader.Rd
d3478b21d05fb56ca42034edb1a34a11 *man/write.mct.Rd
b7d3655956e32050adef55c18b58023d *man/write.pwd.Rd
1a20ae4dfed7dffeedab9d51d15af1bd *man/write_nested_list.Rd
d984318d9aa2557748bde56687225438 *man/write_pwd_list.Rd
01a47d7864d0dc34075ed58a1428fe6c *vignettes/Vignette_polymapR.Rmd
5125ad19a7cabfc9914d8dbc4dc262e0 *vignettes/bibliography.bib
2a525a4d0bfde9865b47c532ce586782 *vignettes/biomed-central.csl
6b4955e241d15d48f601b17efb676552 *vignettes/figures/figure2.png
7cc64231f7e0b635b4302672b0c9c172 *vignettes/figures/map_diagnostics.png
bdb5d220d0b1d4e9311b51bd4c08dda2 *vignettes/polymapR_vignette.RData