/
MD5
138 lines (138 loc) · 7.76 KB
/
MD5
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
242232c4e6ce835a98252f05c611646c *DESCRIPTION
8837236d8550a89081f361a1fdadc3fb *NAMESPACE
ae1eee25e55ec4ca6c5a18e484a88805 *NEWS.md
874560dff337c9a6b1f0be9c3adc5424 *R/check_chrom_lengths.R
f03ed398613c19f17763810b97de5534 *R/check_gsp_for_validity_and_saturation.R
ff7f6ddb6732817970cc73c2952ea708 *R/check_pedigree_for_inbreeding.R
19e945f43ea900512e9a807ea14f9531 *R/check_rec_rates_formatting.R
b176fef33143ad9e84d63e92257f3586 *R/check_reppop.R
d645304aa7f1ec3a3db3aa8db46fb154 *R/computeQs_from_segments.R
44a9f73b68037790f42575a98676abf0 *R/create_GSP.R
67c3d1ca7b2b35945b883c6b9f283ce9 *R/data.R
537568559074d3817d284276dc10a995 *R/drop-segs-down-gsp.R
e0337f8eceba23b9f5059a269d44a2a5 *R/gscramble2newhybrids.R
7f6d44d9385a6e1ec96f8492d2206073 *R/gscramble2plink.R
45bf71c472b7324520ab2e8cdfac5c50 *R/gsp2dot.R
6f551559a2623e84969d1fe3dd92a26e *R/import.R
1e4bd927eb02bbc052dfa9a329ef3aab *R/make_subscript_matrix.R
c6bcbeb9149230073993074f6bef8a92 *R/mat_scramble.R
86e12f69790532992ee7fa0ff93d748a *R/perm_gs_by_pops.R
4d5857c6352510a6a3129225ff6b6d52 *R/plink2gscramble.R
15022afcf3605a84761aceaee5eb3b44 *R/plink_map2rec_rates.R
e46e76a4fef41bbead0df4ccfa452dfe *R/plot_simulated_chromosome_segments.R
c9e77d9306699e78f0a485a2407767de *R/prep_gsp_for_hap_dropping.R
f2a1ba24b24ec5583a4bf925dee9134e *R/rearrange_genos.R
edf66bb48f94b535b5bb3265876cc733 *R/recomb_point.R
f2b8f37d8fb11dae2d24c9ab76f9afad *R/renumber_GSP.R
daeb9d3328bbb9bc1ff3896e7a879a5b *R/seg2tib.R
8dd60aea0c2dd7a82b913343ce0727e1 *R/seg_haps_through_gsp.R
c7d751489f2528cbc2d88f724be79b4d *R/segments2markers.R
2d1ee4aeca17eb338f5bda612826bf8b *R/segregate.R
7dc19eec5b6ae274b49b61e0b9516699 *R/sim_level_founder_haplos.R
05f3214d59a91c617d12d9325742d0fc *R/tidy_up_sampled_haplos.R
2c68e7f4defdea45d0ab6afa4ac8f7ae *R/xover.R
7914f531085ed0d1b2de1b3f3fb0ddc0 *README.md
6a7251e2ab4483658a97936d1e4135d5 *build/vignette.rds
5ec63e0b1a1fe93e6f5e5c9fb8b7f708 *data/GSP.rda
58c867b648a32f4bd87f5d129adec7df *data/GSP_opts.rda
2fe3e4ddbaaf617e60a4fdecca83b1eb *data/Geno.rda
93b480ccd30fcad64673bb1878712d8b *data/I_meta.rda
3f984d62d046caa326e4449ae066ae5d *data/M_meta.rda
f98e75f2299576dfcc40385e0e3b562f *data/RecRates.rda
370d25ed3ecdbcbd0923d87397382ee2 *data/RepPop1.rda
09d29909bb4e82e80222e3d2a8f18671 *data/RepPop4.rda
05d34bb66d7298943f267c46cad448d6 *data/example_chrom_lengths.rda
e736d331993aab86814c321a430a93e0 *data/example_segements.rda
fc942d7a6b291ffa6955e437be330edb *data/gsp3.rda
16aefe845d5bf3ccd4765b530b42afbf *data/gsp4.rda
64ceebc7c799dca364f1becdf962fbb8 *inst/doc/about-createGSP.R
0d30360731c6f779e95ff0f538583a1d *inst/doc/about-createGSP.Rmd
7899fc53e5b46b70c63e71260a5c4ad6 *inst/doc/about-createGSP.html
bcd6f735ed44b7747406f34b38ca0d15 *inst/doc/gscramble-tutorial.R
ac7f21ab391c348b447d0ef60305af5d *inst/doc/gscramble-tutorial.Rmd
101a3061ae0a08bcb7bb4a5d82328cc8 *inst/doc/gscramble-tutorial.html
122de78f8426b70ba400861b43ed1cc5 *inst/doc/permutation-options.R
e7467c7a9dfc2e83b2141b6801cc4925 *inst/doc/permutation-options.Rmd
daf8aee989287f9f28b01376fade5f83 *inst/doc/permutation-options.html
788c8ffab94288d4742d2a356a637a4f *inst/extdata/13-member-ped-with-errors.csv
449e2d297d551b84ffbf2fb741d3c091 *inst/extdata/13-member-ped.csv
d3dddcbe1d28dabef1a80d00e6605875 *inst/extdata/Torterau_et_al_2012_sus_scrofa_map.txt.gz
b09d9aaa82ed5f932f07e3d835b10e39 *inst/extdata/another-ped.csv
a45ed328afbb5cf80fa412792b4bbc4b *inst/extdata/eight_BX2s.csv
c3130adf2ec607bd3a07f317a31e0bb6 *inst/extdata/example-plink-with-morgans.map.gz
5bada0b0634477ab591d73ab9bdce4af *inst/extdata/example-plink.map.gz
d641903ef45970d307a5ed531758fe31 *inst/extdata/example-plink.ped.gz
f35bf80da17cfe930fd9a1ec62774f76 *inst/extdata/four_BX1s.csv
0980bb5e7bac5c22d96251db97ee0928 *inst/extdata/gsp3.csv
6e8c8d74efcecc87c01e43a4331f78e8 *inst/extdata/gsp4.csv
056f7ca2719d43cca0f994985fd07381 *inst/extdata/two_F1s.csv
61f458fb8784281ad824b33cc6ea98bf *man/GSP.Rd
b18ead72349dfe3a3e22d28bef1ade2d *man/GSP_opts.Rd
1cca857c10ff894844e11d7eb2a4d318 *man/Geno.Rd
03bba7012fb408061c5a7554bcb6e7b2 *man/I_meta.Rd
652c4f8cd1591b91a0542e1ea98dd838 *man/M_meta.Rd
9bf4d7faccd64d7d2188b52337de3158 *man/RecRates.Rd
8697f06004c04a70f30813e715686977 *man/RepPop1.Rd
6dcdf5a603740505cf0fa0f106b21755 *man/RepPop4.Rd
4027df2e57a1f1ca29d2f062727c48d9 *man/check_chrom_lengths.Rd
5801b77a9992b1369098afb6c66de98b *man/check_gsp_for_validity_and_saturation.Rd
3d2c85f1cffccbd254dfa511f0c48633 *man/check_pedigree_for_inbreeding.Rd
c9bb7ec52bd34b0f8a1f6a48320f7f82 *man/check_rec_rates_formatting.Rd
3a6ac256ad2fc1588f5ee6fe4f1efed6 *man/check_reppop.Rd
d2a943ce3c3890268bf59a4f0babcd84 *man/computeQs_from_segments.Rd
f7f411efce3d95234b96da4900cddd8c *man/create_GSP.Rd
62d3dcef3e73e19b0539b38125f50043 *man/drop_segs_down_gsp.Rd
39dbd6abab510756f0f3c8b27984d870 *man/example_chrom_lengths.Rd
27f0d01508dc9b895470bf067ce4f9da *man/example_segments.Rd
830ca2bb527b6ba5a17698fa260d128d *man/figures/1.svg
7dbdd147dbc1515f9cec842dc4c7117a *man/figures/10.svg
fc46d3f81a5ad6c60762b65a8a19b56f *man/figures/11.svg
26e2638db6e961ba8e00c63a0ea0062e *man/figures/12.svg
af379fbd9ca37d65bc9c6b1ff2f3a6d6 *man/figures/13-member-ped.svg
7def9231f92c04ea07997f8b18f6f7ea *man/figures/13.svg
3154dbad42f9131911cc761476659727 *man/figures/14.svg
8bc3fa3bca35deccfefcef01efb746c0 *man/figures/15.svg
bc634108cf696a91d33a9b572762c2ff *man/figures/2.svg
061ac60640fa46ecf3ab7fbd708da38f *man/figures/3.svg
f0a63c571c9128b68345ec12de9b7e15 *man/figures/4.svg
24407f20b032d9bdd3ed9749b88189e1 *man/figures/5.svg
41152f7bae8d8093bc99a4a376bee5ad *man/figures/6.svg
e5b6c288557ed4de0d7a17e53d204c42 *man/figures/7.svg
8ecc95abadf169266dded63c567cb1bd *man/figures/8.svg
fce1337318e997d71067d39506a41e6c *man/figures/9.svg
6260684c7f9339babb1294605adfda08 *man/figures/F1-500.png
d3cec0c923a67697f7ab2d9b6b072812 *man/figures/gsp4-700.png
041cd232231051b94723ed5bd14e2474 *man/gscramble2newhybrids.Rd
050ac21946e96df2e3f290d581108b7a *man/gscramble2plink.Rd
ff975d1f5f452950a5a0528e4d354be1 *man/gsp2dot.Rd
9162e17e9f3b6ef1b80eb16d18e92c7e *man/gsp3.Rd
a350affe9f68658675c7abe860c16d9c *man/gsp4.Rd
232116f05a9562c585e748751931b4ce *man/make_subscript_matrix.Rd
1be6483e0e96772f0e5a58f6737f3941 *man/mat_scramble.Rd
622d13590f80d822e1b73a36bacc6c63 *man/perm_gs_by_pops.Rd
09526690dd713a95c7d67a460c6295c5 *man/plink2gscramble.Rd
3e152c75249ef5a2f84ac0b34da21e76 *man/plink_map2rec_rates.Rd
089b7354b900a3c5531014fa80278729 *man/plot_simulated_chromomsome_segments.Rd
884edd5b53349627b5ad28a25c789cd5 *man/prep_gsp_for_hap_dropping.Rd
1c1fb8c8ffc46540fa5fe03e2ab94057 *man/rearrange_genos.Rd
562514b675a506fb24cc5e5fe51508ed *man/recomb_point.Rd
a341f504237ce775f812bd88c116c9fd *man/renumber_GSP.Rd
a1c6491d65eae450d97d4f60e65bc764 *man/seg2tib.Rd
35808cf9a6da3f2e49b443db2e840703 *man/seg_haps_through_gsp.Rd
f7dfb8bd474045600b06780ddcc9b7e1 *man/segments2markers.Rd
e9c3f7a1c56ea86f51a2f61ea24347aa *man/segregate.Rd
c9ab10e1be4a6efb700c0c642436584e *man/sim_level_founder_haplos.Rd
23bf0dd48b3f317760278951067a27ce *man/tidy_up_sampled_haplos.Rd
7a7722c3f09019dbab30f949404683f8 *man/xover.Rd
0d30360731c6f779e95ff0f538583a1d *vignettes/about-createGSP.Rmd
ac7f21ab391c348b447d0ef60305af5d *vignettes/gscramble-tutorial.Rmd
8dd6a772a0e539a1ad0dbc4382040948 *vignettes/images/13-member-ped.svg
7def9231f92c04ea07997f8b18f6f7ea *vignettes/images/13.svg
6260684c7f9339babb1294605adfda08 *vignettes/images/F1-500.png
d0fd91167dc9694712092c36baea1040 *vignettes/images/eight-BX2s-500.png
81c8684d078b78364ae2dc3774e70e80 *vignettes/images/four-BX1s-500.png
9332755b35b72954ec4b3e4c5b3dae33 *vignettes/images/gsp3-500.png
319e22438bf01aecd99de79c97479149 *vignettes/images/gsp3.png
d3cec0c923a67697f7ab2d9b6b072812 *vignettes/images/gsp4-700.png
52ae78c5133f0d3c87169a48e0dcb1f7 *vignettes/images/ped13_complex.svg
e7467c7a9dfc2e83b2141b6801cc4925 *vignettes/permutation-options.Rmd