18  Genetic Power Calculator

18.1 Background

These power calculations are useful for genetic case control studies They use the gap package and pbsize2 command

citation Jing Hua Zhao (2013). gap: Genetic Analysis Package. R package version 1.1-10

18.2 Libraries

library(gap)

Loading required package: gap.datasets

gap version 1.6

library(knitr)

18.3 Usage

18.3.1 Define study characteristics

prevalence=0.1
alpha=0.05
num.cases=2000
num.controls=2000
num.total=num.cases+num.controls
prop.cases=num.cases/num.total

18.3.2 Define ranges of minor allele frequency and effect sizes

maf_values<-seq(0.01,0.49,by=0.01)
risk_values<-seq(1,1.6,by=0.01)

18.3.3 Calculate power at all possible combinations

x<-matrix(nrow=length(risk_values),ncol=length(maf_values))

for (i in 1:length(risk_values)){risk = risk_values[i];for (j in 1:length(maf_values)){maf = maf_values[j];try(x[i,j]<-pbsize2(N=num.total,fc=prop.cases,alpha=alpha,gamma=risk,p=maf,kp=prevalence,model="additive"))}}

18.3.4 Define a matrix which contains the results

xx<-as.data.frame(x,row.names=as.character(risk_values));names(xx)<-as.character(maf_values)

kable(xx)

	0.01	0.02	0.03	0.04	0.05	0.06	0.07	0.08	0.09	0.1	0.11	0.12	0.13	0.14	0.15	0.16	0.17	0.18	0.19	0.2	0.21	0.22	0.23	0.24	0.25	0.26	0.27	0.28	0.29	0.3	0.31	0.32	0.33	0.34	0.35	0.36	0.37	0.38	0.39	0.4	0.41	0.42	0.43	0.44	0.45	0.46	0.47	0.48	0.49
1	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000	0.0500000
1.01	0.0501394	0.0502758	0.0504094	0.0505402	0.0506680	0.0507930	0.0509151	0.0510343	0.0511507	0.0512642	0.0513748	0.0514826	0.0515875	0.0516896	0.0517887	0.0518851	0.0519786	0.0520692	0.0521569	0.0522418	0.0523239	0.0524031	0.0524795	0.0525530	0.0526237	0.0526916	0.0527566	0.0528187	0.0528781	0.0529346	0.0529882	0.0530391	0.0530871	0.0531323	0.0531747	0.0532142	0.0532509	0.0532849	0.0533160	0.0533443	0.0533698	0.0533924	0.0534123	0.0534294	0.0534437	0.0534551	0.0534638	0.0534697	0.0534728
1.02	0.0505549	0.0510983	0.0516302	0.0521506	0.0526594	0.0531566	0.0536424	0.0541166	0.0545792	0.0550304	0.0554700	0.0558980	0.0563146	0.0567196	0.0571131	0.0574951	0.0578655	0.0582245	0.0585720	0.0589080	0.0592325	0.0595455	0.0598471	0.0601372	0.0604159	0.0606832	0.0609390	0.0611834	0.0614165	0.0616381	0.0618483	0.0620472	0.0622348	0.0624110	0.0625759	0.0627295	0.0628718	0.0630028	0.0631226	0.0632312	0.0633285	0.0634146	0.0634895	0.0635532	0.0636058	0.0636473	0.0636776	0.0636968	0.0637050
1.03	0.0512433	0.0524609	0.0536530	0.0548193	0.0559599	0.0570746	0.0581635	0.0592265	0.0602636	0.0612747	0.0622599	0.0632190	0.0641521	0.0650591	0.0659401	0.0667951	0.0676240	0.0684268	0.0692036	0.0699543	0.0706789	0.0713776	0.0720502	0.0726969	0.0733176	0.0739123	0.0744811	0.0750240	0.0755410	0.0760322	0.0764976	0.0769372	0.0773511	0.0777394	0.0781020	0.0784390	0.0787504	0.0790364	0.0792969	0.0795320	0.0797417	0.0799262	0.0800854	0.0802195	0.0803285	0.0804124	0.0804713	0.0805052	0.0805144
1.04	0.0522012	0.0543582	0.0564707	0.0585383	0.0605609	0.0625382	0.0644700	0.0663560	0.0681962	0.0699903	0.0717382	0.0734398	0.0750949	0.0767036	0.0782656	0.0797810	0.0812497	0.0826717	0.0840469	0.0853752	0.0866568	0.0878917	0.0890797	0.0902210	0.0913156	0.0923635	0.0933648	0.0943196	0.0952279	0.0960897	0.0969052	0.0976744	0.0983974	0.0990744	0.0997053	0.1002904	0.1008298	0.1013234	0.1017716	0.1021743	0.1025317	0.1028440	0.1031113	0.1033337	0.1035114	0.1036444	0.1037331	0.1037774	0.1037776
1.05	0.0534259	0.0567856	0.0600782	0.0633027	0.0664583	0.0695444	0.0725602	0.0755051	0.0783785	0.0811802	0.0839095	0.0865661	0.0891497	0.0916600	0.0940969	0.0964600	0.0987492	0.1009645	0.1031057	0.1051728	0.1071657	0.1090844	0.1109290	0.1126995	0.1143960	0.1160185	0.1175672	0.1190422	0.1204436	0.1217716	0.1230263	0.1242080	0.1253168	0.1263529	0.1273165	0.1282079	0.1290273	0.1297749	0.1304510	0.1310558	0.1315896	0.1320527	0.1324453	0.1327677	0.1330203	0.1332032	0.1333168	0.1333614	0.1333372
1.06	0.0549148	0.0597397	0.0644721	0.0691099	0.0736510	0.0780937	0.0824362	0.0866773	0.0908155	0.0948499	0.0987794	0.1026031	0.1063204	0.1099307	0.1134334	0.1168282	0.1201146	0.1232926	0.1263620	0.1293225	0.1321743	0.1349173	0.1375517	0.1400775	0.1424949	0.1448042	0.1470055	0.1490993	0.1510857	0.1529652	0.1547380	0.1564046	0.1579654	0.1594208	0.1607712	0.1620171	0.1631589	0.1641971	0.1651322	0.1659646	0.1666949	0.1673235	0.1678510	0.1682778	0.1686045	0.1688316	0.1689595	0.1689889	0.1689201
1.07	0.0566656	0.0632174	0.0696502	0.0759589	0.0821393	0.0881877	0.0941006	0.0998752	0.1055088	0.1109993	0.1163447	0.1215436	0.1265945	0.1314963	0.1362483	0.1408497	0.1453001	0.1495991	0.1537466	0.1577426	0.1615871	0.1652803	0.1688226	0.1722142	0.1754558	0.1785477	0.1814906	0.1842851	0.1869319	0.1894316	0.1917852	0.1939932	0.1960566	0.1979761	0.1997525	0.2013868	0.2028797	0.2042321	0.2054449	0.2065189	0.2074550	0.2082540	0.2089168	0.2094442	0.2098370	0.2100962	0.2102224	0.2102166	0.2100794
1.08	0.0586762	0.0672167	0.0756109	0.0838493	0.0919236	0.0998267	0.1075524	0.1150951	0.1224505	0.1296145	0.1365840	0.1433562	0.1499292	0.1563012	0.1624709	0.1684376	0.1742007	0.1797600	0.1851154	0.1902674	0.1952163	0.1999629	0.2045079	0.2088523	0.2129971	0.2169435	0.2206928	0.2242462	0.2276052	0.2307711	0.2337453	0.2365294	0.2391248	0.2415330	0.2437555	0.2457938	0.2476493	0.2493235	0.2508178	0.2521337	0.2532725	0.2542357	0.2550244	0.2556402	0.2560842	0.2563577	0.2564618	0.2563979	0.2561670
1.09	0.0609447	0.0717356	0.0823531	0.0927803	0.1030025	0.1130072	0.1227836	0.1323228	0.1416172	0.1506607	0.1594481	0.1679757	0.1762403	0.1842398	0.1919728	0.1994385	0.2066365	0.2135673	0.2202314	0.2266299	0.2327642	0.2386358	0.2442467	0.2495988	0.2546944	0.2595358	0.2641253	0.2684655	0.2725589	0.2764080	0.2800153	0.2833835	0.2865152	0.2894127	0.2920786	0.2945154	0.2967254	0.2987109	0.3004743	0.3020178	0.3033434	0.3044532	0.3053493	0.3060334	0.3065075	0.3067734	0.3068326	0.3066869	0.3063377
1.1	0.0634695	0.0767725	0.0898755	0.1027499	0.1153713	0.1277191	0.1397763	0.1515287	0.1629649	0.1740757	0.1848540	0.1952944	0.2053934	0.2151485	0.2245584	0.2336231	0.2423432	0.2507201	0.2587559	0.2664532	0.2738149	0.2808446	0.2875457	0.2939223	0.2999783	0.3057180	0.3111456	0.3162653	0.3210815	0.3255985	0.3298204	0.3337516	0.3373960	0.3407576	0.3438405	0.3466482	0.3491845	0.3514529	0.3534568	0.3551993	0.3566836	0.3579125	0.3588890	0.3596155	0.3600946	0.3603287	0.3603198	0.3600702	0.3595817
1.11	0.0662489	0.0823259	0.0981762	0.1137539	0.1290205	0.1439443	0.1584994	0.1726649	0.1864244	0.1997654	0.2126787	0.2251578	0.2371987	0.2487996	0.2599605	0.2706827	0.2809689	0.2908228	0.3002490	0.3092526	0.3178395	0.3260159	0.3337882	0.3411633	0.3481479	0.3547491	0.3609738	0.3668288	0.3723210	0.3774572	0.3822438	0.3866873	0.3907937	0.3945692	0.3980193	0.4011496	0.4039654	0.4064715	0.4086729	0.4105738	0.4121786	0.4134912	0.4145154	0.4152544	0.4157116	0.4158900	0.4157921	0.4154206	0.4147777
1.12	0.0692815	0.0883940	0.1072521	0.1257848	0.1439344	0.1616540	0.1789061	0.1956617	0.2118987	0.2276008	0.2427572	0.2573610	0.2714092	0.2849018	0.2978410	0.3102315	0.3220793	0.3333921	0.3441784	0.3544476	0.3642096	0.3734749	0.3822541	0.3905581	0.3983976	0.4057835	0.4127264	0.4192366	0.4253244	0.4309996	0.4362718	0.4411501	0.4456434	0.4497600	0.4535079	0.4568947	0.4599275	0.4626132	0.4649579	0.4669677	0.4686480	0.4700038	0.4710400	0.4717607	0.4721700	0.4722713	0.4720679	0.4715625	0.4707578
1.13	0.0725659	0.0949751	0.1170986	0.1388317	0.1600902	0.1808077	0.2009328	0.2204265	0.2392608	0.2574164	0.2748815	0.2916506	0.3077232	0.3231030	0.3377969	0.3518148	0.3651682	0.3778706	0.3899366	0.4013815	0.4122212	0.4224721	0.4321504	0.4412723	0.4498540	0.4579112	0.4654592	0.4725128	0.4790865	0.4851940	0.4908484	0.4960624	0.5008476	0.5052156	0.5091767	0.5127411	0.5159179	0.5187159	0.5211431	0.5232071	0.5249145	0.5262717	0.5272844	0.5279576	0.5282961	0.5283039	0.5279845	0.5273410	0.5263761
1.14	0.0761009	0.1020668	0.1277094	0.1528786	0.1774564	0.2013520	0.2244972	0.2468425	0.2683541	0.2890110	0.3088028	0.3277274	0.3457894	0.3629992	0.3793711	0.3949226	0.4096738	0.4236464	0.4368632	0.4493479	0.4611242	0.4722160	0.4826469	0.4924401	0.5016182	0.5102030	0.5182156	0.5256761	0.5326038	0.5390170	0.5449330	0.5503682	0.5553378	0.5598564	0.5639374	0.5675933	0.5708357	0.5736753	0.5761219	0.5781846	0.5798715	0.5811900	0.5821467	0.5827475	0.5829976	0.5829014	0.5824628	0.5816849	0.5805704
1.15	0.0798850	0.1096662	0.1390758	0.1679049	0.1959929	0.2232197	0.2494984	0.2747688	0.2989930	0.3221507	0.3442357	0.3652529	0.3852160	0.4041452	0.4220659	0.4390068	0.4549994	0.4700767	0.4842723	0.4976204	0.5101549	0.5219092	0.5329156	0.5432058	0.5528100	0.5617572	0.5700749	0.5777895	0.5849256	0.5915066	0.5975542	0.6030890	0.6081299	0.6126948	0.6167999	0.6204604	0.6236902	0.6265019	0.6289072	0.6309164	0.6325391	0.6337835	0.6346571	0.6351663	0.6353169	0.6351134	0.6345598	0.6336592	0.6324138
1.16	0.0839170	0.1177696	0.1511866	0.1838840	0.2156497	0.2463297	0.2758169	0.3040421	0.3309658	0.3565724	0.3808643	0.4038582	0.4255813	0.4460685	0.4653603	0.4835005	0.5005357	0.5165130	0.5314800	0.5454837	0.5585701	0.5707838	0.5821678	0.5927630	0.6026084	0.6117410	0.6201956	0.6280048	0.6351992	0.6418074	0.6478559	0.6533693	0.6583704	0.6628801	0.6669176	0.6705005	0.6736448	0.6763652	0.6786745	0.6805847	0.6821061	0.6832479	0.6840182	0.6844238	0.6844706	0.6841634	0.6835058	0.6825008	0.6811502
1.17	0.0881956	0.1263727	0.1640275	0.2007837	0.2363675	0.2705871	0.3033160	0.3344783	0.3640380	0.3919894	0.4183498	0.4431534	0.4664467	0.4882846	0.5087274	0.5278387	0.5456834	0.5623265	0.5778320	0.5922622	0.6056771	0.6181340	0.6296874	0.6403889	0.6502868	0.6594265	0.6678502	0.6755974	0.6827046	0.6892054	0.6951310	0.7005100	0.7053685	0.7097306	0.7136180	0.7170506	0.7200462	0.7226208	0.7247889	0.7265632	0.7279550	0.7289738	0.7296283	0.7299253	0.7298709	0.7294695	0.7287246	0.7276388	0.7262133
1.18	0.0927193	0.1354700	0.1775816	0.2185655	0.2580770	0.2958842	0.3318428	0.3658757	0.3979570	0.4280984	0.4563395	0.4827392	0.5073700	0.5303127	0.5516528	0.5714780	0.5898757	0.6069315	0.6227285	0.6373463	0.6508603	0.6633418	0.6748578	0.6854707	0.6952386	0.7042154	0.7124508	0.7199908	0.7268774	0.7331492	0.7388416	0.7439867	0.7486139	0.7527496	0.7564178	0.7596402	0.7624360	0.7648225	0.7668149	0.7684268	0.7696697	0.7705537	0.7710873	0.7712775	0.7711300	0.7706491	0.7698378	0.7686979	0.7672302
1.19	0.0974867	0.1450549	0.1918283	0.2371848	0.2806999	0.3221009	0.3612308	0.3980188	0.4324578	0.4645866	0.4944759	0.5222179	0.5479185	0.5716908	0.5936510	0.6139152	0.6325967	0.6498049	0.6656439	0.6802120	0.6936012	0.7058975	0.7171804	0.7275233	0.7369940	0.7456546	0.7535617	0.7607673	0.7673185	0.7732584	0.7786256	0.7834556	0.7877799	0.7916271	0.7950228	0.7979900	0.8005488	0.8027173	0.8045113	0.8059444	0.8070286	0.8077738	0.8081884	0.8082792	0.8080515	0.8075089	0.8066542	0.8054883	0.8040112
1.2	0.1024962	0.1551198	0.2067440	0.2565910	0.3041490	0.3491070	0.3913026	0.4306820	0.4672685	0.5011391	0.5324063	0.5612050	0.5876821	0.6119899	0.6342803	0.6547020	0.6733974	0.6905018	0.7061417	0.7204351	0.7334911	0.7454102	0.7562842	0.7661973	0.7752260	0.7834399	0.7909020	0.7976692	0.8037931	0.8093199	0.8142914	0.8187450	0.8227142	0.8262289	0.8293155	0.8319978	0.8342965	0.8362299	0.8378138	0.8390618	0.8399857	0.8405952	0.8408984	0.8409014	0.8406090	0.8400245	0.8391498	0.8379851	0.8365296
1.21	0.1077461	0.1656557	0.2223016	0.2767274	0.3283292	0.3767630	0.4218725	0.4636342	0.5021162	0.5374468	0.5697920	0.5993391	0.6262843	0.6508252	0.6731546	0.6934570	0.7119065	0.7286653	0.7438835	0.7576987	0.7702367	0.7816119	0.7919279	0.8012783	0.8097476	0.8174115	0.8243382	0.8305889	0.8362181	0.8412746	0.8458020	0.8498391	0.8534204	0.8565762	0.8593335	0.8617161	0.8637447	0.8654373	0.8668095	0.8678745	0.8686437	0.8691261	0.8693293	0.8692590	0.8689192	0.8683125	0.8674400	0.8663015	0.8648952
1.22	0.1132344	0.1766524	0.2384707	0.2975320	0.3531385	0.4049228	0.4527499	0.4966438	0.5367335	0.5732136	0.6063161	0.6362908	0.6633912	0.6878658	0.7099522	0.7298735	0.7478367	0.7640318	0.7786318	0.7917937	0.8036587	0.8143541	0.8239936	0.8326791	0.8405012	0.8475407	0.8538697	0.8595519	0.8646440	0.8691962	0.8732529	0.8768532	0.8800318	0.8828191	0.8852416	0.8873228	0.8890827	0.8905388	0.8917061	0.8925971	0.8932224	0.8935904	0.8937079	0.8935799	0.8932098	0.8925994	0.8917492	0.8906583	0.8893241
1.23	0.1189591	0.1880984	0.2552176	0.3189377	0.3784692	0.4334357	0.4837429	0.5294827	0.5708637	0.6081628	0.6416910	0.6717702	0.6987185	0.7228402	0.7444206	0.7637228	0.7809870	0.7964304	0.8102481	0.8226146	0.8336853	0.8435981	0.8524754	0.8604251	0.8675426	0.8739122	0.8796080	0.8846951	0.8892312	0.8932664	0.8968452	0.9000063	0.9027836	0.9052069	0.9073017	0.9090906	0.9105927	0.9118245	0.9128000	0.9135309	0.9140268	0.9142954	0.9143426	0.9141726	0.9137882	0.9131906	0.9123795	0.9113532	0.9101089
1.24	0.1249179	0.1999805	0.2725053	0.3408728	0.4042090	0.4621484	0.5146613	0.5619309	0.6042662	0.6420430	0.6756638	0.7055322	0.7320364	0.7555404	0.7763786	0.7948543	0.8112401	0.8257788	0.8386856	0.8501504	0.8603402	0.8694016	0.8774631	0.8846369	0.8910213	0.8967020	0.9017537	0.9062419	0.9102234	0.9137479	0.9168585	0.9195927	0.9219833	0.9240584	0.9258426	0.9273567	0.9286187	0.9296440	0.9304453	0.9310332	0.9314163	0.9316015	0.9315938	0.9313967	0.9310121	0.9304407	0.9296816	0.9287327	0.9275907
1.25	0.1311085	0.2122844	0.2902939	0.3632618	0.4302427	0.4909075	0.5453199	0.5937806	0.6367209	0.6746322	0.7080207	0.7373793	0.7631712	0.7858216	0.8057144	0.8231919	0.8385568	0.8520750	0.8639791	0.8744715	0.8837282	0.8919017	0.8991242	0.9055101	0.9111585	0.9161548	0.9205732	0.9244776	0.9279233	0.9309581	0.9336235	0.9359549	0.9379831	0.9397347	0.9412321	0.9424949	0.9435393	0.9443794	0.9450265	0.9454901	0.9457779	0.9458955	0.9458473	0.9456360	0.9452629	0.9447281	0.9440303	0.9431669	0.9421342
1.26	0.1375280	0.2249943	0.3085409	0.3860260	0.4564533	0.5195620	0.5755418	0.6248398	0.6680318	0.7057415	0.7385893	0.7671636	0.7920051	0.8136006	0.8323818	0.8487274	0.8629672	0.8753868	0.8862325	0.8957159	0.9040190	0.9112974	0.9176846	0.9232949	0.9282262	0.9325623	0.9363750	0.9397259	0.9426676	0.9452455	0.9474982	0.9494590	0.9511563	0.9526143	0.9538536	0.9548919	0.9557438	0.9564216	0.9569356	0.9572940	0.9575031	0.9575681	0.9574922	0.9572776	0.9569250	0.9564341	0.9558031	0.9550292	0.9541084
1.27	0.1441736	0.2380932	0.3272010	0.4090844	0.4827238	0.5479651	0.6051609	0.6549347	0.6980299	0.7352170	0.7672397	0.7947857	0.8184740	0.8388513	0.8563938	0.8715128	0.8845611	0.8958396	0.9056046	0.9140734	0.9214304	0.9278317	0.9334098	0.9382766	0.9425272	0.9462421	0.9494899	0.9523285	0.9548074	0.9569685	0.9588477	0.9604751	0.9618768	0.9630743	0.9640864	0.9649285	0.9656136	0.9661525	0.9665541	0.9668252	0.9669716	0.9669970	0.9669044	0.9666951	0.9663694	0.9659266	0.9653646	0.9646806	0.9638705
1.28	0.1510420	0.2515624	0.3462269	0.4323544	0.5089386	0.5759765	0.6340241	0.6839128	0.7265748	0.7629407	0.7938838	0.8201929	0.8425636	0.8615987	0.8778146	0.8916500	0.9034757	0.9136035	0.9222953	0.9297703	0.9362123	0.9417753	0.9465879	0.9507584	0.9543773	0.9575209	0.9602531	0.9626278	0.9646906	0.9664797	0.9680276	0.9693614	0.9705042	0.9714754	0.9722912	0.9729652	0.9735088	0.9739311	0.9742396	0.9744403	0.9745378	0.9745351	0.9744344	0.9742367	0.9739419	0.9735489	0.9730556	0.9724590	0.9717550
1.29	0.1581299	0.2653824	0.3655692	0.4557525	0.5349846	0.6034643	0.6619938	0.7116440	0.7535556	0.7888301	0.8184737	0.8433755	0.8643038	0.8819121	0.8967510	0.9092810	0.9198850	0.9288810	0.9365320	0.9430558	0.9486324	0.9534110	0.9575150	0.9610468	0.9640915	0.9667199	0.9689909	0.9709538	0.9726497	0.9741130	0.9753726	0.9764525	0.9773730	0.9781509	0.9788004	0.9793331	0.9797587	0.9800849	0.9803181	0.9804631	0.9805236	0.9805021	0.9804002	0.9802184	0.9799563	0.9796126	0.9791853	0.9786713	0.9780667
1.3	0.1654335	0.2795320	0.3851773	0.4791957	0.5607531	0.6303063	0.6889491	0.7380216	0.7788910	0.8128367	0.8409987	0.8643624	0.8837627	0.8998971	0.9133434	0.9245771	0.9339879	0.9418945	0.9485573	0.9541890	0.9589633	0.9630224	0.9664827	0.9694397	0.9719721	0.9741445	0.9760105	0.9776142	0.9789923	0.9801753	0.9811883	0.9820525	0.9827852	0.9834011	0.9839120	0.9843279	0.9846568	0.9849053	0.9850785	0.9851805	0.9852140	0.9851811	0.9850828	0.9849194	0.9846902	0.9843939	0.9840283	0.9835906	0.9830771
1.31	0.1729487	0.2939891	0.4049990	0.5026015	0.5861403	0.6563918	0.7147866	0.7629630	0.8025286	0.8349444	0.8614816	0.8832155	0.9010398	0.9156877	0.9277565	0.9377297	0.9459981	0.9528765	0.9586186	0.9634289	0.9674727	0.9708834	0.9737692	0.9762178	0.9783008	0.9800766	0.9815927	0.9828884	0.9839958	0.9849414	0.9857471	0.9864309	0.9870076	0.9874896	0.9878869	0.9882077	0.9884588	0.9886455	0.9887719	0.9888413	0.9888559	0.9888172	0.9887258	0.9885818	0.9883843	0.9881321	0.9878230	0.9874544	0.9870227
1.32	0.1806715	0.3087306	0.4249817	0.5258894	0.6110491	0.6816222	0.7394214	0.7864091	0.8244428	0.8551658	0.8799741	0.9000244	0.9162592	0.9294386	0.9401709	0.9489413	0.9561355	0.9620601	0.9669588	0.9710257	0.9744153	0.9772512	0.9796325	0.9816387	0.9833339	0.9847698	0.9859885	0.9870241	0.9879044	0.9886522	0.9892861	0.9898213	0.9902703	0.9906434	0.9909489	0.9911936	0.9913830	0.9915213	0.9916119	0.9916573	0.9916592	0.9916187	0.9915361	0.9914114	0.9912436	0.9910315	0.9907731	0.9904658	0.9901065
1.33	0.1885971	0.3237322	0.4450723	0.5489813	0.6353896	0.7059119	0.7627873	0.8083232	0.8446337	0.8735395	0.8965527	0.9149002	0.9295629	0.9413177	0.9507759	0.9584174	0.9646179	0.9696719	0.9738103	0.9772145	0.9800273	0.9823616	0.9843066	0.9859334	0.9872987	0.9884479	0.9894174	0.9902365	0.9909291	0.9915143	0.9920078	0.9924224	0.9927684	0.9930542	0.9932866	0.9934711	0.9936122	0.9937132	0.9937768	0.9938050	0.9937989	0.9937594	0.9936867	0.9935803	0.9934396	0.9932632	0.9930493	0.9927957	0.9924994
1.34	0.1967209	0.3389691	0.4652177	0.5718023	0.6590799	0.7291891	0.7848360	0.8286905	0.8631235	0.8901257	0.9113131	0.9279703	0.9411046	0.9514998	0.9597623	0.9663604	0.9716556	0.9759267	0.9793896	0.9822118	0.9845233	0.9864257	0.9879987	0.9893048	0.9903935	0.9913041	0.9920676	0.9927090	0.9932484	0.9937019	0.9940823	0.9944002	0.9946641	0.9948808	0.9950558	0.9951934	0.9952973	0.9953700	0.9954137	0.9954298	0.9954193	0.9953826	0.9953197	0.9952303	0.9951137	0.9949685	0.9947933	0.9945858	0.9943437
1.35	0.2050376	0.3544154	0.4853651	0.5942813	0.6820471	0.7513955	0.8055371	0.8475154	0.8799545	0.9050030	0.9243663	0.9393726	0.9510438	0.9601607	0.9673172	0.9729648	0.9774465	0.9810232	0.9838943	0.9862120	0.9880937	0.9896295	0.9908894	0.9919280	0.9927878	0.9935023	0.9940978	0.9945953	0.9950114	0.9953593	0.9956498	0.9958912	0.9960905	0.9962532	0.9963836	0.9964852	0.9965608	0.9966124	0.9966417	0.9966497	0.9966370	0.9966041	0.9965507	0.9964766	0.9963810	0.9962627	0.9961204	0.9959522	0.9957559
1.36	0.2135418	0.3700448	0.5054628	0.6163516	0.7042271	0.7724864	0.8248765	0.8648203	0.8951858	0.9182640	0.9358334	0.9492512	0.9595415	0.9674728	0.9736200	0.9784129	0.9821732	0.9851420	0.9875010	0.9893874	0.9909051	0.9921335	0.9931334	0.9939516	0.9946243	0.9951797	0.9956399	0.9960221	0.9963401	0.9966046	0.9968243	0.9970060	0.9971551	0.9972761	0.9973723	0.9974466	0.9975009	0.9975370	0.9975560	0.9975587	0.9975456	0.9975168	0.9974723	0.9974115	0.9973339	0.9972385	0.9971239	0.9969887	0.9968308
1.37	0.2222280	0.3858305	0.5254599	0.6379513	0.7255654	0.7924306	0.8428559	0.8806431	0.9088901	0.9300117	0.9458420	0.9577515	0.9667553	0.9736011	0.9788387	0.9828727	0.9860010	0.9884442	0.9903656	0.9918873	0.9931006	0.9940744	0.9948608	0.9954996	0.9960212	0.9964491	0.9968015	0.9970925	0.9973333	0.9975326	0.9976973	0.9978328	0.9979434	0.9980325	0.9981029	0.9981566	0.9981952	0.9982200	0.9982319	0.9982314	0.9982188	0.9981943	0.9981576	0.9981083	0.9980460	0.9979696	0.9978782	0.9977703	0.9976442
1.38	0.2310901	0.4017452	0.5453072	0.6590240	0.7460171	0.8112093	0.8594908	0.8950349	0.9211507	0.9403563	0.9545220	0.9650174	0.9728371	0.9787006	0.9831281	0.9864959	0.9890772	0.9910710	0.9926228	0.9938399	0.9948015	0.9955668	0.9961799	0.9966743	0.9970752	0.9974020	0.9976695	0.9978892	0.9980700	0.9982188	0.9983412	0.9984413	0.9985226	0.9985877	0.9986387	0.9986771	0.9987043	0.9987210	0.9987281	0.9987258	0.9987143	0.9986938	0.9986640	0.9986245	0.9985748	0.9985142	0.9984418	0.9983563	0.9982564
1.39	0.2401221	0.4177614	0.5649573	0.6795186	0.7655466	0.8288160	0.8748092	0.9080577	0.9320589	0.9494114	0.9620030	0.9711876	0.9779298	0.9829145	0.9866284	0.9894181	0.9915309	0.9931448	0.9943878	0.9953532	0.9961090	0.9967053	0.9971793	0.9975587	0.9978642	0.9981117	0.9983130	0.9984775	0.9986121	0.9987224	0.9988126	0.9988860	0.9989452	0.9989924	0.9990290	0.9990562	0.9990751	0.9990862	0.9990900	0.9990868	0.9990768	0.9990599	0.9990359	0.9990046	0.9989653	0.9989176	0.9988607	0.9987934	0.9987148
1.4	0.2493174	0.4338516	0.5843648	0.6993899	0.7841278	0.8452551	0.8888500	0.9197819	0.9417110	0.9572919	0.9684112	0.9763940	0.9821660	0.9863727	0.9894648	0.9917579	0.9934739	0.9947699	0.9957576	0.9965171	0.9971064	0.9975673	0.9979308	0.9982195	0.9984505	0.9986363	0.9987867	0.9989088	0.9990082	0.9990892	0.9991552	0.9992086	0.9992514	0.9992852	0.9993113	0.9993304	0.9993433	0.9993505	0.9993523	0.9993489	0.9993404	0.9993267	0.9993076	0.9992829	0.9992522	0.9992149	0.9991704	0.9991178	0.9990563
1.41	0.2586693	0.4499883	0.6034868	0.7185989	0.8017432	0.8605412	0.9016609	0.9302846	0.9502058	0.9641112	0.9738677	0.9807597	0.9856670	0.9891919	0.9917475	0.9936183	0.9950015	0.9960342	0.9968130	0.9974059	0.9978617	0.9982151	0.9984916	0.9987096	0.9988829	0.9990214	0.9991328	0.9992227	0.9992956	0.9993546	0.9994025	0.9994410	0.9994717	0.9994958	0.9995142	0.9995275	0.9995362	0.9995408	0.9995413	0.9995380	0.9995309	0.9995199	0.9995049	0.9994856	0.9994617	0.9994328	0.9993983	0.9993575	0.9993096
1.42	0.2681711	0.4661442	0.6222829	0.7371124	0.8183843	0.8746979	0.9132973	0.9396469	0.9576429	0.9699792	0.9784864	0.9843980	0.9885420	0.9914751	0.9935723	0.9950876	0.9961942	0.9970110	0.9976204	0.9980797	0.9984295	0.9986985	0.9989072	0.9990706	0.9991995	0.9993019	0.9993838	0.9994496	0.9995026	0.9995453	0.9995798	0.9996074	0.9996292	0.9996463	0.9996591	0.9996683	0.9996741	0.9996769	0.9996767	0.9996737	0.9996679	0.9996592	0.9996475	0.9996326	0.9996141	0.9995918	0.9995652	0.9995337	0.9994966
1.43	0.2778154	0.4822921	0.6407157	0.7549031	0.8340500	0.8877564	0.9238203	0.9479525	0.9641203	0.9750009	0.9823736	0.9874119	0.9908884	0.9933125	0.9950215	0.9962401	0.9971191	0.9977604	0.9982338	0.9985870	0.9988535	0.9990567	0.9992131	0.9993346	0.9994298	0.9995050	0.9995648	0.9996125	0.9996508	0.9996815	0.9997061	0.9997257	0.9997412	0.9997531	0.9997620	0.9997683	0.9997721	0.9997737	0.9997732	0.9997706	0.9997659	0.9997591	0.9997500	0.9997385	0.9997244	0.9997073	0.9996869	0.9996627	0.9996342
1.44	0.2875951	0.4984053	0.6587505	0.7719499	0.8487472	0.8997550	0.9332949	0.9552859	0.9697332	0.9792754	0.9856267	0.9898940	0.9927917	0.9947818	0.9961651	0.9971383	0.9978316	0.9983317	0.9986967	0.9989664	0.9991679	0.9993203	0.9994366	0.9995263	0.9995962	0.9996510	0.9996943	0.9997287	0.9997561	0.9997781	0.9997955	0.9998094	0.9998202	0.9998285	0.9998347	0.9998389	0.9998414	0.9998422	0.9998416	0.9998394	0.9998357	0.9998304	0.9998234	0.9998146	0.9998039	0.9997908	0.9997753	0.9997568	0.9997350
1.45	0.2975025	0.5144578	0.6763558	0.7882372	0.8624890	0.9107371	0.9417893	0.9617307	0.9745727	0.9828945	0.9883339	0.9919263	0.9943263	0.9959496	0.9970618	0.9978339	0.9983770	0.9987642	0.9990437	0.9992482	0.9993996	0.9995130	0.9995989	0.9996648	0.9997156	0.9997553	0.9997865	0.9998111	0.9998306	0.9998462	0.9998585	0.9998682	0.9998757	0.9998815	0.9998857	0.9998885	0.9998901	0.9998905	0.9998898	0.9998880	0.9998851	0.9998810	0.9998757	0.9998691	0.9998609	0.9998510	0.9998392	0.9998252	0.9998086
1.46	0.3075301	0.5304240	0.6935034	0.8037552	0.8752948	0.9207509	0.9493728	0.9673688	0.9787251	0.9859429	0.9905747	0.9935809	0.9955565	0.9968723	0.9977608	0.9983693	0.9987919	0.9990896	0.9993023	0.9994562	0.9995691	0.9996530	0.9997161	0.9997640	0.9998008	0.9998294	0.9998516	0.9998691	0.9998830	0.9998939	0.9999025	0.9999093	0.9999145	0.9999185	0.9999213	0.9999232	0.9999241	0.9999243	0.9999236	0.9999222	0.9999199	0.9999168	0.9999128	0.9999078	0.9999017	0.9998942	0.9998853	0.9998747	0.9998621
1.47	0.3176698	0.5462791	0.7101681	0.8184990	0.8871892	0.9298475	0.9561150	0.9722789	0.9822707	0.9884976	0.9924196	0.9949206	0.9965371	0.9975970	0.9983023	0.9987788	0.9991055	0.9993330	0.9994937	0.9996088	0.9996925	0.9997541	0.9998001	0.9998348	0.9998612	0.9998816	0.9998974	0.9999098	0.9999195	0.9999272	0.9999332	0.9999379	0.9999415	0.9999441	0.9999461	0.9999473	0.9999479	0.9999479	0.9999473	0.9999461	0.9999444	0.9999421	0.9999391	0.9999353	0.9999307	0.9999251	0.9999184	0.9999104	0.9999009
1.48	0.3279138	0.5619993	0.7263283	0.8324690	0.8982014	0.9380806	0.9620850	0.9765361	0.9852839	0.9906278	0.9939306	0.9959994	0.9973143	0.9981630	0.9987194	0.9990902	0.9993412	0.9995139	0.9996345	0.9997201	0.9997817	0.9998267	0.9998600	0.9998849	0.9999038	0.9999183	0.9999295	0.9999381	0.9999449	0.9999503	0.9999544	0.9999576	0.9999601	0.9999619	0.9999632	0.9999640	0.9999643	0.9999642	0.9999637	0.9999629	0.9999615	0.9999598	0.9999575	0.9999547	0.9999513	0.9999471	0.9999421	0.9999361	0.9999289
1.49	0.3382540	0.5775616	0.7419655	0.8456701	0.9083642	0.9455052	0.9673499	0.9802113	0.9878327	0.9923953	0.9951617	0.9968635	0.9979270	0.9986025	0.9990388	0.9993256	0.9995172	0.9996475	0.9997375	0.9998007	0.9998458	0.9998785	0.9999024	0.9999202	0.9999337	0.9999439	0.9999517	0.9999578	0.9999625	0.9999662	0.9999690	0.9999712	0.9999729	0.9999741	0.9999750	0.9999755	0.9999756	0.9999755	0.9999752	0.9999745	0.9999735	0.9999722	0.9999705	0.9999684	0.9999659	0.9999628	0.9999590	0.9999546	0.9999492
1.5	0.3486820	0.5929440	0.7570643	0.8581112	0.9177137	0.9521768	0.9719748	0.9833703	0.9899789	0.9938549	0.9961598	0.9975521	0.9984073	0.9989419	0.9992821	0.9995026	0.9996480	0.9997457	0.9998125	0.9998589	0.9998917	0.9999152	0.9999323	0.9999450	0.9999545	0.9999616	0.9999671	0.9999713	0.9999746	0.9999771	0.9999791	0.9999805	0.9999817	0.9999825	0.9999830	0.9999834	0.9999834	0.9999833	0.9999830	0.9999825	0.9999818	0.9999808	0.9999795	0.9999780	0.9999761	0.9999738	0.9999711	0.9999677	0.9999637
1.51	0.3591896	0.6081256	0.7716127	0.8698055	0.9262883	0.9581507	0.9760217	0.9860744	0.9917780	0.9950544	0.9969650	0.9980980	0.9987820	0.9992027	0.9994664	0.9996349	0.9997446	0.9998175	0.9998667	0.9999005	0.9999243	0.9999411	0.9999533	0.9999623	0.9999689	0.9999739	0.9999777	0.9999806	0.9999828	0.9999846	0.9999859	0.9999869	0.9999877	0.9999882	0.9999886	0.9999887	0.9999888	0.9999887	0.9999884	0.9999880	0.9999875	0.9999868	0.9999859	0.9999847	0.9999833	0.9999817	0.9999796	0.9999771	0.9999741
1.52	0.3697684	0.6230866	0.7856017	0.8807691	0.9341283	0.9634813	0.9795492	0.9883795	0.9932795	0.9960358	0.9976115	0.9985286	0.9990727	0.9994020	0.9996052	0.9997333	0.9998156	0.9998696	0.9999057	0.9999302	0.9999473	0.9999593	0.9999679	0.9999742	0.9999788	0.9999823	0.9999849	0.9999869	0.9999885	0.9999896	0.9999905	0.9999912	0.9999917	0.9999921	0.9999923	0.9999924	0.9999924	0.9999923	0.9999921	0.9999919	0.9999915	0.9999909	0.9999903	0.9999894	0.9999884	0.9999872	0.9999857	0.9999838	0.9999816
1.53	0.3804099	0.6378087	0.7990252	0.8910214	0.9412750	0.9682217	0.9826126	0.9903364	0.9945272	0.9968349	0.9981280	0.9988666	0.9992972	0.9995535	0.9997093	0.9998061	0.9998675	0.9999073	0.9999336	0.9999513	0.9999635	0.9999720	0.9999781	0.9999825	0.9999857	0.9999881	0.9999899	0.9999912	0.9999923	0.9999931	0.9999937	0.9999941	0.9999945	0.9999947	0.9999948	0.9999949	0.9999949	0.9999948	0.9999947	0.9999945	0.9999942	0.9999938	0.9999933	0.9999927	0.9999920	0.9999910	0.9999899	0.9999886	0.9999869
1.54	0.3911058	0.6522744	0.8118800	0.9005844	0.9477703	0.9724231	0.9852629	0.9919911	0.9955595	0.9974827	0.9985388	0.9991307	0.9994696	0.9996681	0.9997869	0.9998597	0.9999052	0.9999344	0.9999534	0.9999662	0.9999748	0.9999808	0.9999851	0.9999881	0.9999903	0.9999920	0.9999932	0.9999941	0.9999948	0.9999954	0.9999958	0.9999961	0.9999963	0.9999965	0.9999966	0.9999966	0.9999966	0.9999965	0.9999964	0.9999962	0.9999960	0.9999958	0.9999954	0.9999950	0.9999944	0.9999938	0.9999929	0.9999920	0.9999907
1.55	0.4018474	0.6664678	0.8241657	0.9094823	0.9536565	0.9761345	0.9875476	0.9933848	0.9964102	0.9980056	0.9988640	0.9993360	0.9996014	0.9997543	0.9998445	0.9998989	0.9999325	0.9999538	0.9999675	0.9999766	0.9999827	0.9999869	0.9999899	0.9999920	0.9999935	0.9999946	0.9999955	0.9999961	0.9999966	0.9999969	0.9999972	0.9999974	0.9999975	0.9999976	0.9999977	0.9999977	0.9999977	0.9999977	0.9999976	0.9999975	0.9999973	0.9999971	0.9999968	0.9999965	0.9999961	0.9999957	0.9999951	0.9999943	0.9999934
1.56	0.4126264	0.6803742	0.8358843	0.9177408	0.9589751	0.9794022	0.9895101	0.9945541	0.9971082	0.9984259	0.9991203	0.9994948	0.9997018	0.9998189	0.9998870	0.9999275	0.9999521	0.9999676	0.9999774	0.9999839	0.9999882	0.9999911	0.9999932	0.9999946	0.9999957	0.9999964	0.9999970	0.9999974	0.9999977	0.9999980	0.9999981	0.9999983	0.9999984	0.9999984	0.9999985	0.9999985	0.9999985	0.9999984	0.9999984	0.9999983	0.9999982	0.9999980	0.9999978	0.9999976	0.9999973	0.9999970	0.9999966	0.9999960	0.9999954
1.57	0.4234342	0.6939803	0.8470401	0.9253874	0.9637673	0.9822702	0.9911898	0.9955314	0.9976787	0.9987622	0.9993214	0.9996173	0.9997778	0.9998671	0.9999182	0.9999482	0.9999662	0.9999773	0.9999844	0.9999889	0.9999920	0.9999940	0.9999954	0.9999964	0.9999971	0.9999976	0.9999980	0.9999983	0.9999985	0.9999987	0.9999988	0.9999989	0.9999989	0.9999990	0.9999990	0.9999990	0.9999990	0.9999990	0.9999989	0.9999988	0.9999988	0.9999987	0.9999985	0.9999984	0.9999982	0.9999979	0.9999976	0.9999972	0.9999967
1.58	0.4342624	0.7072742	0.8576399	0.9324505	0.9680730	0.9847793	0.9926225	0.9963452	0.9981431	0.9990302	0.9994786	0.9997111	0.9998351	0.9999029	0.9999411	0.9999631	0.9999762	0.9999842	0.9999892	0.9999924	0.9999945	0.9999960	0.9999969	0.9999976	0.9999981	0.9999984	0.9999987	0.9999989	0.9999990	0.9999991	0.9999992	0.9999993	0.9999993	0.9999993	0.9999993	0.9999993	0.9999993	0.9999993	0.9999993	0.9999992	0.9999992	0.9999991	0.9999990	0.9999989	0.9999987	0.9999986	0.9999983	0.9999980	0.9999977
1.59	0.4451027	0.7202450	0.8676921	0.9389591	0.9719310	0.9869677	0.9938403	0.9970203	0.9985197	0.9992429	0.9996008	0.9997828	0.9998781	0.9999293	0.9999577	0.9999739	0.9999834	0.9999891	0.9999926	0.9999949	0.9999963	0.9999973	0.9999979	0.9999984	0.9999987	0.9999990	0.9999991	0.9999993	0.9999994	0.9999994	0.9999995	0.9999995	0.9999995	0.9999996	0.9999996	0.9999996	0.9999996	0.9999995	0.9999995	0.9999995	0.9999994	0.9999994	0.9999993	0.9999992	0.9999991	0.9999990	0.9999988	0.9999986	0.9999984
1.6	0.4559468	0.7328836	0.8772072	0.9449428	0.9753783	0.9888704	0.9948720	0.9975784	0.9988238	0.9994111	0.9996955	0.9998374	0.9999102	0.9999487	0.9999698	0.9999816	0.9999884	0.9999925	0.9999950	0.9999965	0.9999975	0.9999982	0.9999986	0.9999989	0.9999992	0.9999993	0.9999994	0.9999995	0.9999996	0.9999996	0.9999997	0.9999997	0.9999997	0.9999997	0.9999997	0.9999997	0.9999997	0.9999997	0.9999997	0.9999997	0.9999996	0.9999996	0.9999995	0.9999995	0.9999994	0.9999993	0.9999992	0.9999990	0.9999989

18.3.5 Define a palette for the results

#set the colours used for the plot
wut.colors<-rev(c("red","magenta","pink","orange","yellow","green","dark green", "blue","purple","dark blue"))

#print plot of power

image(risk_values,maf_values,as.matrix(xx),zlim=c(0,1),col= wut.colors,breaks=seq(0,1,by=0.1),useRaster=T,main=paste("Power @ Prevalence :",prevalence,"| Cases :",num.cases,"| Controls :",num.controls,"| alpha :",alpha),xlab="Relative Risk",ylab="Minor allele frequency",cex.main=0.8);legend(x=1,y=0.4,cex=0.5,legend=c("0.00-0.09","0.10-0.19","0.20-0.29","0.30-0.39","0.40-0.49","0.50-0.59","0.60-0.69","0.70-0.79","0.80-0.89","0.90-1.00"),fill=wut.colors,title="Power")