Description Usage Details Examples
Examples of the MangroveORs
, MangroveBetas
and MangrovePed
classes from the Mangrove
package. To be used in combination with the Mangrove vignette.
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See vignette("Mangrove") for details on these example objects.
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A Mangrove pedigree.
Number of individuals: 20000
Number of genotyped individuals: 20000
Number of affecteds: 10000
Number of markers: 4
Allele counts:
SNP1 SNP2 SNP3 SNP4
AA: 1136 AA:6574 AA:2696 CC: 1
AC: 7049 CA:9597 AC:9153 CG: 387
CC:11815 CC:3829 CC:8151 GG:19612
A Mangrove pedigree.
Number of individuals: 1000
Number of genotyped individuals: 1000
Number of affecteds: 0
Number of markers: 179
Allele counts:
rs2284746 rs1738475 rs4601530 rs7532866 rs2154319 rs17391694 rs6699417
AA:279 AA:165 AA:592 AA:471 AA: 68 AA:763 AA:179
AC:249 AC:217 AT:183 AC:217 AT:191 AT:105 AT:229
CA:244 CA:261 TA:162 CA:201 TA:179 TA:115 TA:235
CC:228 CC:357 TT: 63 CC:111 TT:562 TT: 17 TT:357
rs10874746 rs9428104 rs11205277 rs17346452 rs1325598 rs1046934 rs10863936
AA:390 AA: 62 AA:358 AA: 78 AA:193 AA:411 AA:298
AT:246 AC:186 AC:237 AT:189 AC:254 AC:219 AC:254
TA:233 CA:175 CA:237 TA:187 CA:234 CA:241 CA:241
TT:131 CC:577 CC:168 TT:546 CC:319 CC:129 CC:207
rs6684205 rs11118346 rs10799445 rs4665736 rs6714546 rs17511102 rs2341459
AA:490 AA:283 AA:595 AA:223 AA: 84 AA:839 AA:545
AC:199 AT:250 AC:181 AT:244 AC:197 AC: 76 AT:188
CA:207 TA:237 CA:165 TA:243 CA:227 CA: 80 TA:193
CC:104 TT:230 CC: 59 TT:290 CC:492 CC: 5 TT: 74
rs12474201 rs3791675 rs11684404 rs7567288 rs7567851 rs1351164 rs12470505
AA:127 AA:595 AA:103 AA: 55 AA:842 AA: 37 AA: 8
AC:227 AT:169 AT:199 AT:174 AC: 85 AT:196 AT: 97
CA:239 TA:184 TA:252 TA:136 CA: 71 TA:140 TA:108
CC:407 TT: 52 TT:446 TT:635 CC: 2 TT:627 TT:787
rs2629046 rs2580816 rs12694997 rs2597513 rs13088462 rs2336725 rs9835332
AA:229 AA:676 AA: 60 AA: 9 AA: 2 AA:205 AA:282
AT:250 AT:154 AC:164 AT: 88 AT: 49 AT:251 AC:251
TA:233 TA:136 CA:157 TA:113 TA: 59 TA:234 CA:255
TT:288 TT: 34 CC:619 TT:790 TT:890 TT:310 CC:212
rs17806888 rs9863706 rs6439167 rs9844666 rs724016 rs572169 rs720390 rs2247341
AA: 15 AA:598 AA:630 AA: 67 AA:330 AA:465 AA:147 AA:119
AT: 98 AT:170 AT:176 AC:209 AC:237 AT:222 AC:250 AC:238
TA:122 TA:181 TA:151 CA:205 CA:227 TA:217 CA:231 CA:230
TT:765 TT: 51 TT: 43 CC:519 CC:206 TT: 96 CC:372 CC:413
rs6449353 rs17081935 rs7697556 rs788867 rs10010325 rs7689420 rs955748
AA: 24 AA:636 AA:278 AA:100 AA:232 AA:667 AA: 66
AT:132 AT:156 AT:246 AT:238 AC:252 AT:145 AC:171
TA:122 TA:162 TA:277 TA:211 CA:257 TA:157 CA:198
TT:722 TT: 46 TT:199 TT:451 CC:259 TT: 31 CC:565
rs1173727 rs11958779 rs10037512 rs13177718 rs1582931 rs274546 rs526896
AA:381 AA:478 AA:191 AA:861 AA:204 AA:155 AA: 67
AT:236 AC:227 AT:253 AT: 63 AC:244 AC:238 AT:208
TA:228 CA:210 TA:245 TA: 72 CA:264 CA:230 TA:195
TT:155 CC: 85 TT:311 TT: 4 CC:288 CC:377 TT:530
rs4282339 rs12153391 rs889014 rs422421 rs6879260 rs3812163 rs1047014 rs806794
AA: 39 AA: 60 AA:403 AA:599 AA:365 AA:319 AA: 61 AA:481
AC:152 AC:205 AT:239 AT:185 AT:247 AC:237 AT:193 AC:210
CA:139 CA:198 TA:229 TA:172 TA:229 CA:242 TA:177 CA:215
CC:670 CC:537 TT:129 TT: 44 TT:159 CC:202 TT:569 CC: 94
rs3129109 rs2256183 rs6457620 rs2780226 rs6457821 rs9472414 rs9360921 rs310405
AA:332 AA:195 AA:229 AA: 11 AC: 19 AA: 60 AA: 12 AA:272
AT:247 AC:256 AC:247 AT: 79 CA: 16 AC:171 AT: 98 AC:229
TA:256 CA:255 CA:252 TA: 79 CC:965 CA:191 TA:108 CA:263
TT:165 CC:294 CC:272 TT:831 CC:578 TT:782 CC:236
rs7759938 rs1046943 rs961764 rs1490384 rs6569648 rs7763064 rs543650 rs9456307
AA:102 AA:308 AA:328 AA:271 AA: 56 AA: 89 AA:376 AA: 6
AT:203 AC:258 AC:231 AT:230 AT:189 AC:198 AT:232 AC: 53
TA:238 CA:257 CA:280 TA:235 TA:180 CA:196 TA:234 CA: 56
TT:457 CC:177 CC:161 TT:264 TT:575 CC:517 TT:158 CC:885
rs798489 rs4470914 rs12534093 rs1708299 rs6959212 rs42235 rs822552 rs2110001
AA:478 AA:679 AA: 63 AA: 78 AA:464 AA:461 AA: 66 AA:105
AT:215 AT:143 AC:145 AC:209 AT:216 AT:225 AC:187 AC:204
TA:220 TA:146 CA:179 CA:208 TA:209 TA:214 CA:194 CA:227
TT: 87 TT: 32 CC:613 CC:505 TT:111 TT:100 CC:553 CC:464
rs1013209 rs7460090 rs6473015 rs6470764 rs12680655 rs7864648 rs11144688
AA:524 AA: 14 AA:514 AA:652 AA:161 AA:481 AA: 15
AT:192 AT:116 AC:189 AT:141 AC:256 AT:223 AC:109
TA:213 TA:104 CA:217 TA:162 CA:238 TA:206 CA: 98
TT: 71 TT:766 CC: 80 TT: 45 CC:345 TT: 90 CC:778
rs7853377 rs8181166 rs2778031 rs9969804 rs1257763 rs473902 rs7027110 rs1468758
AA:582 AA:234 AA:575 AA:180 AA: 1 AA: 3 AA: 59 AA:555
AC:200 AC:251 AT:184 AC:267 AC: 31 AT: 79 AC:181 AT:191
CA:171 CA:240 TA:191 CA:247 CA: 43 TA: 77 CA:166 TA:199
CC: 47 CC:275 TT: 50 CC:306 CC:925 TT:841 CC:594 TT: 55
rs751543 rs7466269 rs7849585 rs7909670 rs2145998 rs11599750 rs2237886
AA: 77 AA:406 AA:427 AA:305 AA:223 AA:414 AA:782
AT:219 AC:236 AT:233 AT:267 AC:277 AT:244 AT:101
TA:175 CA:231 TA:225 TA:220 CA:251 TA:212 TA:105
TT:529 CC:127 TT:115 TT:208 CC:249 TT:130 TT: 12
rs7926971 rs1330 rs10838801 rs1814175 rs5017948 rs3782089 rs7112925 rs634552
AA:287 AA:425 AA:478 AA:454 AA: 39 AA:870 AA:429 AA:738
AC:250 AT:245 AC:225 AT:210 AC:124 AT: 58 AT:237 AT:126
CA:249 TA:222 CA:198 TA:224 CA:148 TA: 67 TA:215 TA:123
CC:214 TT:108 CC: 99 TT:112 CC:689 TT: 5 TT:119 TT: 13
rs494459 rs654723 rs2856321 rs10770705 rs2638953 rs2066807 rs1351394
AA:380 AA:400 AA:412 AA:100 AA:103 AA: 3 AA:251
AT:232 AC:247 AC:242 AC:234 AC:209 AC: 65 AT:265
TA:222 CA:224 CA:223 CA:221 CA:232 CA: 64 TA:236
TT:166 CC:129 CC:123 CC:445 CC:456 CC:868 TT:248
rs10748128 rs11107116 rs7971536 rs11830103 rs7332115 rs3118905 rs7319045
AA:416 AA:598 AA:224 AA:614 AA:156 AA: 87 AA:163
AT:252 AT:180 AC:246 AC:176 AT:243 AC:206 AC:233
TA:214 TA:180 CA:269 CA:167 TA:226 CA:210 CA:230
TT:118 TT: 42 CC:261 CC: 43 TT:375 CC:497 CC:374
rs1950500 rs2093210 rs1570106 rs862034 rs7155279 rs16964211 rs7178424
AA:496 AA:167 AA:632 AA:140 AA:417 AC: 41 AA:274
AT:201 AT:249 AT:174 AC:202 AT:230 CA: 53 AT:257
TA:208 TA:250 TA:150 CA:221 TA:213 CC:906 TA:266
TT: 95 TT:334 TT: 44 CC:437 TT:140 TT:203
rs10152591 rs12902421 rs5742915 rs11259936 rs16942341 rs2871865 rs4965598
AA:829 AT: 38 AA:221 AA:221 AA:946 AA: 9 AA:109
AC: 90 TA: 27 AT:214 AC:234 AT: 26 AC:108 AT:223
CA: 75 TT:935 TA:245 CA:227 TA: 28 CA:117 TA:203
CC: 6 TT:320 CC:318 CC:766 TT:465
rs11648796 rs26868 rs1659127 rs8052560 rs4640244 rs3110496 rs3764419
AA:546 AA:220 AA:108 AA:639 AA:375 AA: 86 AA:174
AC:208 AC:247 AC:256 AC:166 AC:238 AC:246 AC:222
CA:185 CA:262 CA:216 CA:150 CA:249 CA:226 CA:259
CC: 61 CC:271 CC:420 CC: 45 CC:138 CC:442 CC:345
rs17780086 rs1043515 rs4986172 rs2072153 rs4605213 rs227724 rs2079795
AA: 22 AA:218 AA:438 AA:502 AA:457 AA:431 AA:474
AC:125 AC:227 AT:222 AC:197 AC:218 AC:232 AT:213
CA:140 CA:257 TA:225 CA:223 CA:220 CA:211 TA:218
CC:713 CC:298 TT:115 CC: 78 CC:105 CC:126 TT: 95
rs2665838 rs11867479 rs4800452 rs9967417 rs17782313 rs12982744 rs7507204
AA: 55 AA:443 AA: 41 AA:194 AA: 62 AA:159 AA:578
AC:193 AT:226 AT:159 AC:218 AT:191 AC:241 AC:182
CA:214 TA:222 TA:149 CA:230 TA:166 CA:252 CA:193
CC:538 TT:109 TT:651 CC:358 TT:581 CC:348 CC: 47
rs891088 rs4072910 rs2279008 rs17318596 rs1741344 rs2145272 rs7274811 rs143384
AA:525 AA:257 AA: 58 AA: 98 AA:137 AA:395 AA:597 AA:319
AC:221 AC:262 AT:193 AC:255 AT:218 AC:221 AT:168 AC:256
CA:188 CA:273 TA:178 CA:239 TA:243 CA:254 TA:176 CA:246
CC: 66 CC:208 TT:571 CC:408 TT:402 CC:130 TT: 59 CC:179
rs237743 rs2834442 rs4821083
AA: 54 AA:415 AA: 31
AC:166 AC:259 AT:130
CA:159 CA:216 TA:116
CC:621 CC:110 TT:723
A Mangrove pedigree.
Number of individuals: 19
Number of genotyped individuals: 9
Number of affecteds: 3
Number of markers: 4
Allele counts:
SNP1 SNP2 SNP3 SNP4
AA:4 AA:1 AA:1 AG:6
AC:4 AC:3 AC:5 GG:3
CC:1 CC:5 CC:3
A Mangrove Odds Ratios object:
Number of variants:4
Mean absolute het OR: 1.55
Mean absolute hom OR: 2.475
Mean risk allele frequency: 0.302
For a common (10%) disease, these variants explain 3.85% of variance
For a rare (0.5%) disease, these variants explain 1.77% of variance
A Mangrove Betas object:
Number of variants:179
Mean absolute beta: 0.035
Mean risk allele frequency: 0.474
These variants explain 8.84% of variance
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