MangroveExamples: Example data for the Mangrove vignette

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

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Details

See vignette("Mangrove") for details on these example objects.

Examples

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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.