4bc04f724b38b937ec5fceaff42da240 *DESCRIPTION
696c824cf2ea976f418528a5e6aa18b3 *NAMESPACE
f133eb88736ee9dc5144116ff564750e *NEWS.md
e6c40cbe94617a5e349f7b2da4a0545d *R/Cape.R
afba44d2a000bfaa7b926903e8df3df8 *R/bin_curve.R
5daa5893d55200598b44060474b2e6c3 *R/bin_vector.R
4165c4fd4cb17f74d38fde3caa9c8ffa *R/calc_delta_errors.R
6ccea26ee0ebacf9c8bb04f83d7f7fe2 *R/calc_emp_p.R
7bf1275504ad62f79c351249e0217420 *R/calc_m.R
f4b3806ecebfca3f318158d8c2299059 *R/calc_p.R
7589574893a15ff82094d6a6d016e4ec *R/cape2mpp.R
25d6ab8cad1045431f295fd7e7f48caa *R/center_std.R
d6c05065c7ec179c6b832cef407a3e59 *R/check_bad_markers.R
5b3a4f93fe5aa22fc73aeb8b6a4e6296 *R/check_communities.R
e2cce3c9505c694389775fb6dcf5b091 *R/check_geno.R
bc359c07c33004d75cf4e292fe608389 *R/check_underscore.R
8fa33cbf9a68ad3cb19f666bd10c1020 *R/chunkV.R
94e79e82b655825f87f2ea93a75538bf *R/colors_from_values.R
6fb96892a28eb6b69e6904caf3b36166 *R/compare_markers.R
d5ccb5002491aa85b7c7d5d2331197c7 *R/consec_pairs.R
310e454af5d6d6ac14213902b7198817 *R/delete_underscore.R
13d8f034bd274c23db18c2d685d682da *R/direct_influence.R
50d9d39f7592e3b7645c9b941c080edb *R/draw_pie.R
08146500c8dd5822a39906014333ad67 *R/error_prop.R
b949da985be8269be2fb5d0cd5374db3 *R/exp_color_fun.R
af0908aacaa7c500966ae2dc29b1b2c5 *R/flatten_array.R
22c7cb6797adb328ae19a2df93d9a69c *R/genome_wide_threshold_1D.R
cb97441b2b9733aac966ed01b7627904 *R/get_allele_colors.R
998c0994ad649947d4bf7f3ee794be59 *R/get_block_allele.R
258a0a6ce7986efc01f9fd7340a14ae8 *R/get_circle.R
80642679864207349e21963f25951fba *R/get_col_num.R
51c695ed0499af520f6629948e48fadc *R/get_color.R
e6dffe2704f18620859955292b2a0952 *R/get_color2.R
3a840bf71d675a3c307fa7d79424e4cb *R/get_concent_circ.R
6134d26e467a8bdefc16be81fabd9cf9 *R/get_covar.R
27a06101efbb8bf54e2bc7b36d5417ed *R/get_eigentraits.R
5ddea14c25d058c0e1fb14b253bffd41 *R/get_geno.R
59ad69a444cd6d3ea05e6c7d050b2157 *R/get_geno_dim.R
25e705fcbf1cc1b60ed6482be56d042c *R/get_geno_with_covar.R
506ce6c4a81b1e0f2f8a65e0c85a6f7b *R/get_interaction_error.R
15ffd1dd441c2e4842fe9030daae0cb6 *R/get_layout_mat.R
b7426dc755719f729b146a6fde3bfe03 *R/get_line.R
60f91f85be5ddb07b017de09a6f0e4b9 *R/get_linearly_independent.R
135b01958c90afc54b952156d9c119de *R/get_marker_chr.R
f24f505ed0f0584aa1cb81ef1e1f4147 *R/get_marker_covar.R
0253d365bfab6024a64e48980767ec59 *R/get_marker_idx.R
55a82b6571f8bd0dd7c93c1daddc57be *R/get_marker_location.R
76e9bdf11fc04b574396453e8a60a331 *R/get_marker_name.R
4ea8470a8907b3c539ef460e482a8a47 *R/get_marker_num.R
727fb0918ecf29b0f65aac7ca9d0290b *R/get_network.R
2bdd89340eb5fcd87d7a5c7234dd099a *R/get_pairs_for_pairscan.R
ff44c98eb756b94af427b6f6c7842dc5 *R/get_pheno.R
40b15d993d931dd0d7a4e03d541615db *R/get_stats_multiallele.R
6a27ecd0268838119362c3fd1fef3165 *R/hist_pheno.R
77da74b8b934e19f7e51e6c0a6ef50a3 *R/image_with_text.R
1a8c673726c49c9d16ccc52a4c48ff3b *R/impute_missing_geno.R
7eedd49192e0e33374a0a80fb614a2b8 *R/kin_adjust.R
9049c20dd8e2d68836a187455673b9b7 *R/kinship.R
c3c82644258bbb06e678d458efbb08d5 *R/linkage_blocks_network.R
f582e34e3d50e364b3b1e4ea2a8f7db2 *R/load_input_and_run_cape.R
4561d395753ffdecad2fe61ae047a725 *R/marker2covar.R
3e13ec19525c1d65bf2b995161c22904 *R/my_image_plot.R
5e170e0e6e1cd659b5cc097688e21b2c *R/norm_pheno.R
4147a5958f79aac83b72d488bce09bb2 *R/one_pairscan_parallel.R
c57bb461ea54cf6f17070cd68d8700e2 *R/one_singlescanDO.R
c6c3d5426fbaeeab3baff8a4baf4fcba *R/pair_matrix.R
9fb61376a38ed063507d6667c85d241c *R/pairscan.R
fe1d293103d2251f768f26df275dabca *R/pairscan_kin.R
4e49ca7a8fd1b36d15fdc4bf0c846ca4 *R/pairscan_noKin.R
3e8711aa64b4ffaceb20fb4b620bad1c *R/pairscan_null.R
4460590f4c2180b7758dad915664080c *R/pairscan_null_kin.R
7145b829facccee39d21153da3977a13 *R/pheatmap_generate_breaks.R
a6d9b71f3a1edfd086f8d877abbe6d4b *R/pheatmap_scale_colours.R
31c5c36ee8617b722e8b184232cbabc9 *R/pheno2covar.R
7875588684f19cb35eb1e86841dd7bc6 *R/plink2cape.R
a9230b203a0eb279d11143ebe455ea73 *R/plot_bars.R
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8df1c1b05d09abd31902abeabb48b3e4 *R/plot_network.R
4db33a5024096a0e97d9f3b3abff6473 *R/plot_pairscan.R
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ddc9259dcc47266b52a187563e16ce46 *R/plot_points.R
50863bd4445e5c7f23db869028d63d7b *R/plot_singlescan.R
185d0d33c894f7af6d3ffaec395d67c4 *R/plot_svd.R
3bab793cb9238577ca4f5e9e441bfa14 *R/plot_trait_circ.R
96c1c35265946685f912c3c06cf26794 *R/plot_variant_influences.R
63001bca95f4a2fca17ffa059d0f9e4a *R/qnorm_pheno.R
4f71873ab4c9a6d4e8d2895cb0b99ff0 *R/qtl2_to_cape.R
f760e1edff99b333df2f332b140caa2c *R/read_parameters.R
adbbd996166b9006693494dd2727fc29 *R/read_population.R
396f76621ce678ae09bbf8e2fb9ae68a *R/remove_ind.R
97058c27c39a7a106a398a437ff81498 *R/remove_kin_ind.R
d13a31b1404195e1cdf6a8f6051cdca8 *R/remove_markers.R
89b97142928ced5132d2e380ab7da124 *R/remove_missing_genotype_data.R
322d886dcbec7341ecd265bd79a28569 *R/remove_unused_markers.R
318479fe591501db36f0b679a02dc8db *R/report_progress.R
930aad89902d5a224cd015241c57fe62 *R/rotate_mat.R
f5a2658ed2a0d5f24e0e354802b70840 *R/run_cape.R
2c8aeb5e9770723fd55d26d1deffbc0f *R/rz_transform.R
a0056407848bbd4ec18a748faee0512f *R/segment_region.R
638a2ba3af5a7b3d0c7a9b29258e0b71 *R/select_eigentraits.R
3c5e7d22126b561a8b75bd65e903a93e *R/select_markers_for_pairscan.R
35fac6aa13080894e8d86a7181551fc7 *R/select_pheno.R
0839a994416fa5c12e4a5f073ec4b063 *R/singlescan.R
83f77137a4edd2bfd85d04d54da47f1b *R/sort_by_then_by.R
79f9a3c6bfda2fc61232731ba3fe80c1 *R/write_population.R
5448f44c8569ca02c18ea3040c40f930 *R/write_variant_influences.R
8e6b49c010c6e145c4bf8e80609555d2 *README.md
777b52d1b8672a86a09857e6b71b3d48 *build/vignette.rds
9e4518063446c019ceb79ef79689ac21 *demo/00Index
82f01a6803c1aa6b9dce3279c013b457 *demo/demo_PLINK/0_plink.parameters_0.yml
a25b0d66e3e66caace67c87eb19bed20 *demo/demo_PLINK/data/test.csv
e594aed37eecac2754294857cdf30dcc *demo/demo_PLINK/data/test.map
69f61f5f338a01709deeb0565e92c707 *demo/demo_PLINK/data/test.ped
3749676bbdc9226e7f2ce500d779ffa5 *demo/demo_PLINK/data/test.pheno
5ea70c17f3989d42585b7f5b02fd18d1 *demo/demo_plink.R
8748271a2d177fe55ab369cafb0a50f0 *demo/demo_qtl.R
038c864efa195013b6a3ebefad0123d0 *demo/demo_qtl/0_NON_NZO.parameters_0.yml
3940e7549e1671e06a6b1f004c639e2f *demo/demo_qtl/data/NON_NZO_Reifsnyder_pgm_CAPE_num.csv
b1165f5fb76aa6ba7570ce9e8d5b2097 *demo/demo_qtl2.R
0727f27aba2c09226608de246e489841 *demo/demo_qtl2/0_iron.parameters_0.yml
3eb1386b105e8bd80c785a954b9887cf *demo/demo_qtl2/data/iron.yaml
81a59343f0999de210d7ae2c765b09a9 *demo/demo_qtl2/data/iron_covar.csv
80872c3409d97cab93e5e9c16b849108 *demo/demo_qtl2/data/iron_geno.csv
e8b5a31b78efa0c09715186ff4b3fe48 *demo/demo_qtl2/data/iron_gmap.csv
882d0cfadae7df2aedb1ea8d428a038e *demo/demo_qtl2/data/iron_pheno.csv
9b48da85886d259a9d60f817a32fa2f2 *demo/demo_qtl2/data/iron_phenocovar.csv
46e7dbbfc6d3173b17044622df023a80 *demo/demo_qtl2/data/iron_pmap.csv
8ef5502edfdfbbd90ebdc88d473b5873 *demo/demo_rds.R
935697ceb5308dc636c6536140ad3bfc *demo/demo_rds/0_NON_NZO.parameters_0.yml
451fbeda5e627641b0ead83fb611d76b *demo/demo_rds/data/cape_data.RDS
26a2d1cc543fae4167a4868f0b66c705 *demo/demo_rds/data/cape_geno.RDS
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9661e4a673aea6221783fa040c0a2f6f *inst/doc/cape.Rmd
3d7a5d9558559918181149e0b9c13911 *inst/doc/cape.html
0e7eac722dfb29d8f3321579c6278345 *man/Cape-class.Rd
fa2946beaac7124c8eef996ac68bd604 *man/bin_curve.Rd
47f31c72042a0b3daef70107de992647 *man/bin_vector.Rd
6fb0b92c242228ab27ea35036de0adf4 *man/calc_delta_errors.Rd
85bb5c8f1259dd0284b437362cf396e9 *man/calc_emp_p.Rd
24065346a4a253d60bf2849142abe0b3 *man/calc_m.Rd
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2872ad47235b152aadf93ffc9a031e74 *man/cape2mpp.Rd
0337bf6b39a37c29a7100614112d709a *man/center_std.Rd
bf6795ad1298280e24f93e2ab34cdf19 *man/check_bad_markers.Rd
a1987557df2ec3df99314c360f7c5d34 *man/check_communities.Rd
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776a50374d43343336b7fb0da03ad814 *man/check_underscore.Rd
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3955eb84ee24ba490276add51b00721c *man/colors_from_values.Rd
594f5667cb3dcd4f7443705749742028 *man/compare_markers.Rd
f6d4539044c2821b971d892ecb1af199 *man/consec_pairs.Rd
5af8cf6613e282ac5d4c91613b852747 *man/delete_underscore.Rd
a430d69e5eb7a062b572c888f8ffc4e5 *man/direct_influence.Rd
be1133f827d23807f6c9fa481eba9094 *man/draw_pie.Rd
42ac37f2526f428e54d702fffa83cbaa *man/error_prop.Rd
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930f435d9d25d56e7aba65489f6ecdbe *man/flatten_array.Rd
4bdab918ffba97ea20a616d9c1f1a31c *man/genome_wide_threshold_1D.Rd
2471848c05e5ee215fe1bbc9ade0cc73 *man/get_allele_colors.Rd
cfe11e29c3c908d6c31a1ab905e94a6f *man/get_block_allele.Rd
3dd2414f58b6344c6597954a59d5e276 *man/get_circle.Rd
614d210b4a14d3e6ea9f94224fff1810 *man/get_col_num.Rd
a9e4b3c63c065ec3a636e75241875424 *man/get_color.Rd
0dbc68d07dfaf587aaeb7dc33ffcfe7d *man/get_color2.Rd
94394a658281e955222ce54bcd551028 *man/get_concent_circ.Rd
672a4c2f887ad0a6303083dd764f2c0f *man/get_covar.Rd
2157966d7a864053fd5d027ca3123344 *man/get_eigentraits.Rd
e87b216199d757a3f40be06d4d161bb4 *man/get_geno.Rd
fef5c156fa661bc74871a396b6f354a4 *man/get_geno_dim.Rd
6b3b2d4d213dbc1a7f39a6c65fa5917c *man/get_geno_with_covar.Rd
87cdd6379ddc8e8cfa04fe71e000a92d *man/get_interaction_error.Rd
1149e41cf4695d5dc11981432d29d33a *man/get_layout_mat.Rd
05e8da776130b76b4a9e95123462cc5d *man/get_line.Rd
67b790ef4f29d40992c820102fade496 *man/get_linearly_independent.Rd
8542d69480b6d103e9c3dd30662f17df *man/get_marker_chr.Rd
19611c8ca84f28ade9c5998326444ab9 *man/get_marker_covar.Rd
c09f27d0b7e7765f1e6a9e064667d56b *man/get_marker_idx.Rd
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8be07743e063fc88e4bb0ea82547f7a1 *man/get_marker_num.Rd
dd9e22e3a8561c204e0b0de2c695906c *man/get_network.Rd
134396c9736f8b4c825dc3e9a491c69c *man/get_pairs_for_pairscan.Rd
7051169f9ed6e4e9d72f0e8d6da611af *man/get_pheno.Rd
25f697e614ed6393abb03b9192fc7f90 *man/get_stats_multiallele.Rd
64b7b6b17ed2d67cf3797de3db32da57 *man/hist_pheno.Rd
945d17b26f4fd068efd68f61a86e99f2 *man/image_with_text.Rd
da2cb3d81a76729b1c461370aa90ea3b *man/impute_missing_geno.Rd
41e90b8f160e49947460ebfd5fa6d4aa *man/kin_adjust.Rd
4c19029b62956f600982e1d168afdeab *man/kinship.Rd
6227b096a59b77c61d3f2ceb6a4a50b4 *man/linkage_blocks_network.Rd
05a2667a6e5b7340f2b5d57f9331d956 *man/load_input_and_run_cape.Rd
5c04cbfa20e04645c69ed93bea5ab59c *man/marker2covar.Rd
aca99ba43952824eb96ff569b89c3404 *man/my_image_plot.Rd
7e129020f651b327ab878ba072b53d96 *man/norm_pheno.Rd
a264cb46953b7418cf828e12a889df8a *man/one_pairscan_parallel.Rd
5e1a419372afece34685d39dcae05b3a *man/one_singlescanDO.Rd
1d95e816b0413e4fa7efc54e08419dc9 *man/pair_matrix.Rd
96947069e93a4bee3d66ceec22ec3dce *man/pairscan.Rd
41c2c6fd45d333949c0aa9b11c2db05e *man/pairscan_kin.Rd
2379eea06ea6d2ce6e7661fb24fd447a *man/pairscan_noKin.Rd
d557d0a2d96a55fced944d8217e297be *man/pairscan_null.Rd
4e65e14261238fb7650a6180d184d331 *man/pairscan_null_kin.Rd
80a169dad2f56dfe493ec0bfbdb657e6 *man/pheatmap_generate_breaks.Rd
7151defaafc6574590277c903a21b76c *man/pheatmap_scale_colours.Rd
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6915a920038fc22c1fc24220ad43ed8a *man/plink2cape.Rd
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50d011064e4c2a4c5538c75c74df1f12 *man/plot_network.Rd
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6e2637475ba5193c45bebd633cb8bac1 *man/plot_pheno_cor.Rd
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50d474706ac8ffc3ee0395f327626f44 *man/plot_singlescan.Rd
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49c9be3675dc57c0c78632ff1246d46c *man/qnorm_pheno.Rd
63bbbd7389b0fe46f5f1d937962d449b *man/qtl2_to_cape.Rd
070f06cc1da2ef58bc493a3ed6e9f996 *man/read_parameters.Rd
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4121b035ed8949ca37228698727ffdf1 *man/remove_markers.Rd
dcdda406819f4986de5003718ae4324e *man/remove_missing_genotype_data.Rd
0c545354a837ee54fb743bdf7f8af8e5 *man/remove_unused_markers.Rd
1bdbb694f750c6ebfef47f7f525c5c20 *man/report_progress.Rd
d9f15d3673eaabe49e13886605b5ee91 *man/rotate_mat.Rd
b0a435955cac3916dbaffa781163878b *man/run_cape.Rd
e54aefce11213eb92c8a0ac99bac9326 *man/rz_transform.Rd
10f1b9c4df37cb2a56ec7efff5d51218 *man/segment_region.Rd
4aa26134c841a482242f0df89686c987 *man/select_eigentraits.Rd
9692f4cad098dd081007c6918b08a60f *man/select_markers_for_pairscan.Rd
be78cbbec57b21bde436a9389916e7c9 *man/select_pheno.Rd
a9683b49cedbcab1190f0ced6afa2a87 *man/singlescan.Rd
4aef8a53e639a6358704c204eb6d71f4 *man/sort_by_then_by.Rd
42c893e1d9a172296a22bf1187855e03 *man/write_population.Rd
2eea9b2963c61525f8681b17b4a7da7f *man/write_variant_influences.Rd
3beb0e34394be92549571614fae5f8d9 *tests/ci-tests.R
1855ed8228a92f5281d115a56d0d0694 *tests/ci-tests.sh
4e4a869254eb1a2f6f96922246ca985f *tests/testthat.R
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