MangroveExamples: Example data for the Mangrove vignette
In Mangrove: Risk Prediction on Trees
Description
Usage
Details
Examples
Description
Examples of the MangroveORs, MangroveBetas and MangrovePed classes from the Mangrove package. To be used in combination with the Mangrove vignette.
Usage
1
2
3
4
5
Details
See vignette("Mangrove") for details on these example objects.
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Example output
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
Mangrove documentation built on May 1, 2019, 9:10 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Details Examples
Description
Examples of the MangroveORs, MangroveBetas and MangrovePed classes from the Mangrove package. To be used in combination with the Mangrove vignette.
Usage
1 2 3 4 5 |
Details
See vignette("Mangrove") for details on these example objects.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
Example output
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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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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