b5a068587bdae9cc071eef9b0c51bb01 *DESCRIPTION
5612be7ec4d486329f7a304d8eb14692 *NAMESPACE
26620d7a4ba1b5eee0eb5c3aabc2399d *NEWS.md
c599454cb7edf992d2ab3c99d0360d86 *R/CCcolors-data.R
fb1f783101a84e5c2068d273808fe06e *R/RcppExports.R
fc665fa6ecfe6bf80c6b3120ddaadd22 *R/add_threshold.R
e68d21608bb47b80d558e9d3e7053810 *R/align_scan1_map.R
56a3d59e1b076bbbdbf4aff0cef1187b *R/arg_util.R
3b575ad3b4e4bd18d13c474429adffd7 *R/assign_allele_codes.R
184682a405425cc4e4879513a0fdf95c *R/batch_cols.R
6a6fc7db8f9d875a0112be96dfec8f21 *R/batch_vec.R
83b72de28808dba783fc9cff74351f88 *R/bayes_int.R
6d92d6ae7cbba643124d0063d388dbea *R/calc_entropy.R
e12dc4f941b4a90a11443c5e5fc6ff3b *R/calc_errorlod.R
5ea9ef53a7b47a77bed9df4f39f85198 *R/calc_geno_freq.R
7cb985e4ad4f4c3ffe5d9f1112df0a34 *R/calc_genoprob.R
3280b30f4c275bc0fc954666a3be2a21 *R/calc_genoprob2.R
bab60f2f8835bbc2447aa913e9688fe7 *R/calc_grid.R
d5a8aa6a46c6c93d3fc7b9c56716a0cf *R/calc_het.R
f11853d8d00031f97357b680914532ab *R/calc_kinship.R
c77d0847ddeec02336b0649060a29f12 *R/calc_raw_summaries.R
6a7ce9ffcbea06d66f21709b077a63aa *R/calc_sdp.R
648754d934cfc49bdabe424711ef1bd0 *R/cbind_calc_genoprob.R
b2af37e0bdbc0dda55b06edaa7bd1be8 *R/cbind_expand.R
98555e234a77cf1755b6e73c3f016cd2 *R/cbind_scan1.R
0c504d0bad6022f9b0de422f2fdf7155 *R/cbind_sim_geno.R
906d9fa60218cb0c19de53579c971c4d *R/cbind_viterbi.R
5804421847520d930604b3a5765e4b91 *R/check_cross2.R
7d0bed9c7399d9a90fc12b34b64aab59 *R/chisq_colpairs.R
7a1b44e2b154dfa7b87e75c2d278fa25 *R/chr_lengths.R
c25dd04ccb82ccc00f0452f6515edf9f *R/clean.R
679e513143a0803812eb00b0a60e9c66 *R/clean_genoprob.R
c6c3c31452afac51ea02e40e2b6e062d *R/clean_scan1.R
c1615a0b2f0fc28e653cae7bb8c9ae81 *R/cluster_util.R
014eb3c242fe9eda16a753815d5cd410 *R/compare_geno.R
f873e347f054e80b12ddee8d25dd4f74 *R/compare_genoprob.R
e48a6e748929fc4bd3106c2b478d61d2 *R/compare_maps.R
3039a74d5b9a004f2dd7df893a6f8486 *R/convert2cross2.R
9d2c6ff616fc1e75cf14e4065bf246b5 *R/count_xo.R
fd1ec752a6a4d6beba6ad4b7a9780ed0 *R/covariates.R
eb9c88fbbde616583d598411d694a917 *R/create_gene_query_func.R
f4ce9d8d9f3cf3b00a24762296e89dd4 *R/create_marker_index.R
ec0ff4e93d7fd43bb889b8967cbb33fc *R/create_snpinfo.R
11b8969e51f0a27d978553be32ead1a9 *R/create_variant_query_func.R
c482189aa324a65c243ec905f397bcb0 *R/decomp_kinship.R
c5dcd686befd353fe9bc768e8bf3b13e *R/dim_calc_genoprob.R
1fdec477e6f7ca9835791e2a76964e6b *R/drop_markers.R
effb6af4fb3e0571d53cdb03682fb11a *R/est_herit.R
a474821ba4d4f7f9ffafdb28cb609f27 *R/est_map.R
b442ad000272dbd5704add7278aaa593 *R/find_common_ids.R
f27a3ea044ba647acc1d751b69d1064c *R/find_ibd_segments.R
78c1a71f5a20f8157fe480995ba18fcf *R/find_index_snp.R
81659a66956281b093fd593270bf71b2 *R/find_map_gaps.R
f83efe03a526a6f14573a1fc814f0357 *R/find_marker.R
4c1b5ce2a85a23d762bb44be12e48c7c *R/find_markerpos.R
5154c9e13f98d781cd9e52214abd7dd6 *R/find_peaks.R
c2e8f7e67d6bb34856f843a6b88c26aa *R/find_peaks_and_bayesint.R
26993ba62489e474bed98a93bfeca2c3 *R/find_peaks_and_lodint.R
2be0366f23ec508d9baaa9989b94af55 *R/fit1.R
002337b034ca84d5b50c7ea4d3211ec3 *R/fit1_pg.R
ea4a950ee935bf8e3de2123acf095c22 *R/genoprob_col2drop.R
6bd291df776b89a950f798f9a58213c1 *R/genoprob_to_alleleprob.R
1aa8252a736425709a13c5aca18a965e *R/genoprob_to_snpprob.R
cf58246355fa1179af5689de594030ec *R/get_common_ids.R
52b104e46e9dafd7517329def9b6f75c *R/get_x_covar.R
21306043c2408d365d553684b99e5c28 *R/guess_phase.R
d2b34413bdd08bbbb89a1d3a9039ecc9 *R/hmm_util.R
f3580033b4d22aeeb9508abdcb7a4fab *R/index_snps.R
b5d3ad9fe70e28367b2d98b4ba407f6a *R/insert_pseudomarkers.R
831df39798ffebbd0a44e7bd6901b0fd *R/interp_genoprob.R
814049932cb8973f46d72806cb7ccdf1 *R/interp_map.R
f26e5f5ec7ef08f3c075ad3158c9166d *R/is_phase_known.R
7229e8ec35616eddac4b75e45ec91771 *R/is_same.R
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6c6d1be16de723439841f3665eb2875b *R/locate_xo.R
1d6eb28d0227ec60af971de1ccf7f561 *R/lod_int.R
3b88dce8dfe680a8991b8d5507674b01 *R/map_functions.R
23c8291fcfc406bc41926df8c36710cd *R/map_to_grid.R
6a22949a03a17bea599c6c7bf5b96c26 *R/mat2strata.R
8d59b1287a0fd7492d5d541d73b503ac *R/max_scan1.R
ce4584e98c062ac75e2a95d395d775c0 *R/maxmarg.R
93e29a922367e31ddbaced17c5a82b16 *R/myround.R
f471181a1486b4cbde50dbdeef9435c9 *R/n_missing.R
3cf96dc2becaa68868920a7300f7d4c0 *R/plot_coef.R
920a754fa9178197b236c7d14cfeeb86 *R/plot_coef_and_lod.R
9385533ec0af1b70002f5e6768a2e6c4 *R/plot_genes.R
5de3c31aa4f488cd17e480e7b8026fb0 *R/plot_genoprob.R
1d878dd48ffe06098031c75593662cba *R/plot_genoprobcomp.R
60799adeb9ae6c6811c0a19df541a8e5 *R/plot_lodpeaks.R
10523eb5c710e1ffa10bc56d1932f1a9 *R/plot_onegeno.R
21c1bdfc4e483255995e82c74a1e69fc *R/plot_peaks.R
9b891b42ce31ed2d92b6dc937b551272 *R/plot_pxg.R
92ad03790b65b7a20857dd914d7b66ce *R/plot_scan1.R
141a0754170465fc02b23501ce251885 *R/plot_snpasso.R
5a2257b53b605f5e418c6475a3e6ef64 *R/plot_snpasso_and_genes.R
144e5dc9ff26fbcba1acfe41e312ed04 *R/predict_snpgeno.R
9ae935f8c012f35e7d993f1064b34b6e *R/probs_to_grid.R
1159c2771b85e8dbc66e9daa287b2a6f *R/pull_genoprobint.R
c200051683c8a29c7cf2fdc074b2bc49 *R/pull_genoprobpos.R
101d175aecc507218cf49cb76f2e55d6 *R/qtl2-internal.R
858041c2bf49b5bf3d92e45e33287d66 *R/qtl2-package.R
4ea40d19c75fc3de6a5a3136ce7e79bb *R/qtl2version.R
be0491daf245cce08dbc05c3c3577ae9 *R/rbind_calc_genoprob.R
dae8acb5809e16d1fe967e2267e318e6 *R/rbind_scan1.R
e3cac3fb23c5cd31f4996619be66f3cb *R/rbind_sim_geno.R
1e7efa7949b76053409d8e271b33c39c *R/rbind_viterbi.R
be2d32154331c32b72ad57bc4cfdcd30 *R/rcbind_scan1perm.R
2d0ff3b2eb01fed46f3a266060b0998e *R/read_cross2.R
b9f2994ca5a75529ea9fa58803df6f80 *R/read_csv.R
e2782d676910880b02945b03d9f6ac64 *R/read_csv_numer.R
c55a2d82b082c70acd1088a6493fb022 *R/read_pheno.R
d2f7c20040a9618063e05980889a784e *R/recode_snps.R
34388afb3061b2725df226547033801b *R/reduce_map_gaps.R
9c64169f6ecfa34df6c59a83d3ea890c *R/reduce_markers.R
15b6b30fe4a2ded3e7a297994ad3ff6a *R/reduce_to_index_snps.R
fa720b7a81ed89aec1c171330a5ee34b *R/replace_ids.R
cb4878f64d1de8bef67c761027431216 *R/scale_kinship.R
fe9f19cbd2a9cd6b6078ed87c9cd7e4f *R/scan1.R
bf129552b20527d271786c2d5d47ef97 *R/scan1_binary.R
d651f26936d8942378e41af90470596c *R/scan1_pg.R
98c54b04b5469330f854b4fd8940c1d4 *R/scan1blup.R
0fe00528353a648598464344037d1fe2 *R/scan1blup_pg.R
d17847bbecaad223035603c977102ddc *R/scan1coef.R
345b7a7a708cd835291fbf2e5d52204d *R/scan1coef_pg.R
14386e86407caa30e44d303932e56918 *R/scan1max.R
c1b820b4bfbbbb6284d2b2b3b4a17bcf *R/scan1max_pg.R
301e89ce0ca4685dbeb6d5d80c3873a9 *R/scan1perm.R
021d11d5513b826962dae71434b094b9 *R/scan1perm_pg.R
33f74ede4d29d6c44a619fba81f4ca8f *R/scan1snps.R
46395b91af9ddcacfda03b55959128b0 *R/sim_geno.R
cab3b55247c20d12594ddb5fa4cb68e7 *R/sim_geno2.R
b189851e40be4b0c43bea80e06ba7de8 *R/snpprob_from_cross.R
99101617a12aca08629ec067c0bcb07b *R/subset_calc_genoprob.R
eae9c4fc9e5009bd41c638087fade04f *R/subset_chr.R
da22e168ea9b1be840588a284681e2ac *R/subset_cross2.R
ac80a2748ca80d51722054493cc0c839 *R/subset_ind.R
5e8769a63deef1924cbafca9a9733334 *R/subset_kinship.R
49bdb2434a11ce92b86786c2a65fe923 *R/subset_scan1.R
ca0e1e234434330a3d068350e83cafcc *R/subset_sim_geno.R
aeae13d7df7a48a7d32633c00d84ef6f *R/subset_viterbi.R
9c45b5eadf9e55c2b91a6151fa9542f3 *R/summary_cross2.R
7907cd4f2b8888643e1d646b42f35701 *R/summary_scan1perm.R
8363246eb16254e0693f78073e51f4d6 *R/test_util.R
c3e2b077c68d8b04bcc631015aed9e89 *R/top_snps.R
cd6cb7f210817e3645bf314a11e3bce7 *R/viridis.R
159d4bb8ddbeb129c588d2799342ca79 *R/viterbi.R
9607e4d061832edae0570e22f36ff9f6 *R/viterbi2.R
955e5208b9564726364b6e3113fb3a34 *R/weights_util.R
2fe0e117d6eb098eead88c557565c727 *R/write_control_file.R
5f342e69d72e1f81eb234a83202f21c7 *R/xpos_scan1.R
791a49f22998730dcd05951a1225ecbc *R/zip_datafiles.R
81e610c9f43de03aad30049424b6c5c9 *README.md
b2fdb9699a79354d8b9bbb360e1086f7 *data/CCcolors.RData
d0542c8fa23394cf58b68c55e848fcf4 *data/CCorigcolors.RData
f122f8b15de8bc2a060878f8b3a035b9 *inst/CITATION
08d7338f3243b4c077acdd65d5dba8a9 *inst/extdata/ReadMe.md
f7de8f12e5490dbfe7b860ae6c0897b6 *inst/extdata/cc_variants_small.sqlite
79328389d282d13b8146170bcf163c72 *inst/extdata/grav2.zip
7773871af9c54163e52f8bb00ff5c590 *inst/extdata/iron.zip
a1636e2b81e18096b9159291518fb794 *inst/extdata/mouse_genes_small.sqlite
f07e657feb740b506e4a08aa62fde4e2 *inst/scripts/ReadMe.md
2ceae5a8d36d5072b3426faf698f0c2f *inst/scripts/create_ccvariants.R
e32b92aee32a10b0490bbabb5f56e2a7 *inst/scripts/create_ccvariants_small.R
0c0773d9ffaa6c7400bc8a9889759deb *inst/scripts/create_mousegenes.R
d56e2025a3ce7641e5fd5e9bcdec91ed *inst/scripts/create_mousegenes_mgi.R
1fdbcc69cb3ffb04f03bd0d7ef3e9924 *inst/scripts/create_mousegenes_small.R
df54a016c08463fbd64241dd722d06a7 *man/CCcolors.Rd
8fcf30d0557c647456caf95d4be40f67 *man/add_threshold.Rd
5badb3da734890bed3160129cad5d1ce *man/basic_summaries.Rd
eb8dc8a13814092032bebc7d10fac166 *man/batch_cols.Rd
0195df40d01e9e61c55f7842a9f30eb5 *man/batch_vec.Rd
bd7751a7f8652725d4004a049d05bdcd *man/bayes_int.Rd
cd75d9c99da24484adefc2f146b78c49 *man/calc_entropy.Rd
28d9dfca22bfbf6db01e5118e2f8859e *man/calc_errorlod.Rd
a98972c4d5c31b2e628a7f1a38039ddd *man/calc_geno_freq.Rd
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4b4d48e7d0fa1a9487638f425b1113f1 *man/calc_grid.Rd
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86a4fb06817182a968a7053ebd972569 *man/calc_raw_founder_maf.Rd
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20f0220252f2aa1487e01e8b7f28802e *man/calc_raw_het.Rd
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fb9eb975ef81fcf1d1f9bf4d3bc9a064 *man/cbind.scan1.Rd
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069ce293bee4fc7c76899a78cc4b5794 *man/cbind_expand.Rd
9b674c0887b86566fdd5df05475ab6f7 *man/check_cross2.Rd
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83655d49cfc19d897ce06c5fab06ae1f *man/clean.Rd
7e197cdec1a49cdf57caf839ae31481c *man/clean_genoprob.Rd
b9ce2701928b805619f9a1450fa4f7c8 *man/clean_scan1.Rd
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3eb158612a69f1c4236a7b39555d0fc8 *man/compare_genoprob.Rd
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784e80817af7bb1365d7fb61794f10c1 *man/convert2cross2.Rd
96841e6eb25ef337cbdaecee04b90cf7 *man/count_xo.Rd
1ed312687a6923b21fbd2d2f25f9b9b1 *man/create_gene_query_func.Rd
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8aec4126aee304cd86011d3da2c2972a *man/create_variant_query_func.Rd
8506138cae59cf3e42b069cb2e0eea82 *man/decomp_kinship.Rd
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8c2748497e4cb84ef34c9693179ac863 *man/fit1.Rd
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024bd822f034953d18b1b0b325989dd0 *man/get_common_ids.Rd
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344ee6b467a2f52ea9dd5dd91152db32 *man/plot_pxg.Rd
dc063199a72ba76048b6e69baa6c696a *man/plot_scan1.Rd
c45e5d5324a00f70253ccb596670a372 *man/plot_snpasso.Rd
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22b7599bb0897ba4e4f5d973faa66688 *man/print.summary.scan1perm.Rd
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79a8d8eb0fc536de9e4cc4830a91e78d *man/qtl2-package.Rd
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