Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
function to compute average homozygosity within a personDescriptionThis function computes average homozygosity (inbreeding) for a set of people, across multiple markers. Can be used for Quality Control (e.g. contamination checks) Usagehom.old(data, snpsubset, idsubset, weight="no") Arguments
DetailsWith "freq" option, for person i inbreeding is estimated with f_i = frac{O_i - E_i)}{(L_i - E_i)} where O_i is observed homozygosity, L_i is the number of SNPs measured in individual i and E_i = Σ_{j=1}^{L_i} (1 - 2 p_j (1 - p_j) frac{T_{Aj}}{T_{Aj}-1}) where T_{Aj} is the numer of measured genotypes at locus j. Only polymorphic loci with number of measured henotypes >1 are used with this option. This measure is the same as used by PLINK (see reference). You should use as many people and markers as possible when estimating inbreeding from marker data. ValueWith option weight="no": A matrix with rows corresponding to the ID names and colums showing the number of genotypes measured (NoMeasured) and homozygosity (Hom). With option weight="freq": the same as above + expected homozygosity (E(Hom)) and the estimate of inbreeding, F. Author(s)Yurii Aulchenko ReferencesPurcell S. et al, (2007) PLINK: a toolset for whole genome association and population-based linkage analyses. Am. J. Hum. Genet. See Also
Examplesrequire(GenABEL.data) data(ge03d2) h <- hom(ge03d2[,c(1:100)]) homsem <- h[,"Hom"]*(1-h[,"Hom"])/h[,"NoMeasured"] plot(h[,"Hom"],homsem) # wrong analysis: one should use all people (for right frequency) # and markers (for right F) available! h <- hom(ge03d2[,c(1:10)]) h Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(GenABEL)
Loading required package: MASS
Loading required package: GenABEL.data
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GenABEL/hom.old.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hom.old
> ### Title: function to compute average homozygosity within a person
> ### Aliases: hom.old
> ### Keywords: htest
>
> ### ** Examples
>
> require(GenABEL.data)
> data(ge03d2)
> h <- hom(ge03d2[,c(1:100)])
> homsem <- h[,"Hom"]*(1-h[,"Hom"])/h[,"NoMeasured"]
> plot(h[,"Hom"],homsem)
> # wrong analysis: one should use all people (for right frequency)
> # and markers (for right F) available!
> h <- hom(ge03d2[,c(1:10)])
> h
NoMeasured NoPoly Hom E(Hom) Var F
id4 10 10 0.6000000 0.7028379 1.1494105 -0.346066496
id10 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id25 10 10 0.5000000 0.7028379 0.3812431 -0.682583120
id33 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id35 10 10 0.8000000 0.7028379 0.3836568 0.326966752
id58 10 10 0.9000000 0.7028379 0.9390481 0.663483376
id68 10 10 0.5000000 0.7028379 0.5094701 -0.682583120
id74 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id107 9 9 0.5555556 0.7218390 0.3921547 -0.597795860
id119 10 10 0.7000000 0.7028379 0.1971621 -0.009549872
id145 10 10 0.7000000 0.7028379 0.3953192 -0.009549872
id188 9 9 0.5555556 0.6813169 0.2422528 -0.394628394
id193 10 10 0.9000000 0.7028379 1.1135183 0.663483376
id199 9 9 0.5555556 0.6813169 0.2209190 -0.394628394
id266 10 10 0.7000000 0.7028379 0.5689556 -0.009549872
id287 10 10 0.5000000 0.7028379 0.5803635 -0.682583120
id300 10 10 1.0000000 0.7028379 0.5713693 1.000000000
id327 10 10 1.0000000 0.7028379 2.2844469 1.000000000
id345 10 10 0.9000000 0.7028379 0.5399210 0.663483376
id386 10 10 0.7000000 0.7028379 0.3739278 -0.009549872
id392 10 10 1.0000000 0.7028379 0.5611040 1.000000000
id403 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id415 9 9 0.6666667 0.7103816 1.2992306 -0.150939901
id496 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id497 10 10 0.4000000 0.7028379 0.7377958 -1.019099744
id504 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id542 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id575 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id586 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id608 10 10 0.5000000 0.7028379 0.5094701 -0.682583120
id617 10 10 1.0000000 0.7028379 0.5713693 1.000000000
id660 10 10 0.8000000 0.7028379 0.3836568 0.326966752
id666 9 9 0.4444444 0.7180257 0.5931586 -0.970234543
id689 10 10 0.5000000 0.7028379 0.3812431 -0.682583120
id722 10 10 0.7000000 0.7028379 0.6633935 -0.009549872
id765 10 10 1.0000000 0.7028379 0.5713693 1.000000000
id780 10 10 0.7000000 0.7028379 0.9210849 -0.009549872
id796 10 10 0.6000000 0.7028379 1.3037499 -0.346066496
id802 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id812 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id830 9 9 0.7777778 0.6777010 0.3504668 0.310509022
id835 9 9 0.7777778 0.7103816 0.6958690 0.232706732
id892 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id908 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id938 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id980 10 10 0.6000000 0.7028379 0.4643844 -0.346066496
id994 10 10 0.5000000 0.7028379 0.3598517 -0.682583120
id1047 10 10 0.7000000 0.7028379 0.5689556 -0.009549872
id1052 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id1055 10 10 0.9000000 0.7028379 0.9390481 0.663483376
id1068 10 10 1.0000000 0.7028379 0.5611040 1.000000000
id1076 10 10 0.8000000 0.7028379 0.3239595 0.326966752
id1109 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id1156 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id1176 10 10 0.8000000 0.7028379 0.7675396 0.326966752
id1186 10 10 0.8000000 0.7028379 0.3836568 0.326966752
id1193 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id1251 10 10 0.8000000 0.7028379 0.6004040 0.326966752
id1265 10 10 0.8000000 0.7028379 0.3686705 0.326966752
id1382 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id1394 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id1408 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id1423 10 10 0.8000000 0.7028379 0.3686705 0.326966752
id1457 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id1469 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id1477 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id1505 10 10 0.6000000 0.7028379 0.1832190 -0.346066496
id1509 10 10 1.0000000 0.7028379 0.5116720 1.000000000
id1514 10 10 0.8000000 0.7028379 0.3836568 0.326966752
id1591 10 10 1.0000000 0.7028379 0.6208013 1.000000000
id1593 10 10 0.6000000 0.7028379 0.2238108 -0.346066496
id1653 10 10 1.0000000 0.7028379 0.5611040 1.000000000
id1656 9 9 0.4444444 0.6702937 0.6446107 -0.685001157
id1737 10 10 0.6000000 0.7028379 0.2238108 -0.346066496
id1760 10 10 0.5000000 0.7028379 0.5803635 -0.682583120
id1784 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id1827 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id1841 10 10 1.0000000 0.7028379 0.5611040 1.000000000
id1895 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id1897 10 10 0.5000000 0.7028379 0.7850652 -0.682583120
id1910 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id1918 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id1950 9 9 0.5555556 0.7235764 0.1481409 -0.607838342
id1983 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id1995 10 10 0.9000000 0.7028379 0.3895955 0.663483376
id2012 10 10 0.5000000 0.7028379 0.7850652 -0.682583120
id2049 10 10 0.6000000 0.7028379 0.1832190 -0.346066496
id2054 10 10 0.7000000 0.7028379 0.7019036 -0.009549872
id2056 10 10 0.9000000 0.7028379 0.5399210 0.663483376
id2068 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id2089 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id2094 10 10 0.6000000 0.7028379 0.1832190 -0.346066496
id2097 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id2115 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id2126 10 10 0.6000000 0.7028379 0.6507471 -0.346066496
id2151 10 10 0.8000000 0.7028379 0.3686705 0.326966752
id2173 10 10 0.8000000 0.7028379 0.3836568 0.326966752
id2242 10 10 1.0000000 0.7028379 0.5611040 1.000000000
id2245 10 10 0.7000000 0.7028379 0.9210849 -0.009549872
id2317 10 10 0.5000000 0.7028379 0.3598517 -0.682583120
id2328 10 10 0.7000000 0.7028379 0.7466146 -0.009549872
id2348 9 9 0.7777778 0.7180257 0.3082653 0.211906183
id2351 10 10 0.8000000 0.7028379 0.3686705 0.326966752
id2428 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id2444 10 10 0.7000000 0.7028379 0.5475642 -0.009549872
id2476 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id2514 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id2520 10 10 0.6000000 0.7028379 0.1832190 -0.346066496
id2524 10 10 0.5000000 0.7028379 0.5094701 -0.682583120
id2531 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id2558 10 10 0.5000000 0.7028379 0.3598517 -0.682583120
id2589 8 8 0.6250000 0.6830457 0.2046006 -0.183135819
id2618 10 10 0.5000000 0.7028379 0.3598517 -0.682583120
id2653 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id2654 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id2681 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id2689 10 10 0.6000000 0.7028379 0.1832190 -0.346066496
id2693 10 10 1.0000000 0.7028379 0.5713693 1.000000000
id2708 10 10 0.5000000 0.7028379 0.1000777 -0.682583120
id2741 10 10 0.5000000 0.7028379 0.3598517 -0.682583120
id2842 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id2862 8 8 0.7500000 0.7475450 0.1514464 0.009724319
id2878 10 10 0.9000000 0.7028379 0.4954679 0.663483376
id2894 9 9 0.4444444 0.7180257 0.5931586 -0.970234543
id2901 10 10 0.8000000 0.7028379 0.6004040 0.326966752
id2925 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id2932 10 10 1.0000000 0.7028379 3.1266941 1.000000000
id2973 10 10 0.7000000 0.7028379 0.5475642 -0.009549872
id2985 10 10 0.7000000 0.7028379 0.9210849 -0.009549872
id3021 10 10 0.5000000 0.7028379 0.6560044 -0.682583120
id3056 10 10 0.5000000 0.7028379 0.1000777 -0.682583120
id3111 10 10 1.0000000 0.7028379 0.6208013 1.000000000
id3129 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id3139 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id3176 10 10 0.7000000 0.7028379 0.9210849 -0.009549872
id3189 10 10 0.7000000 0.7028379 0.3522084 -0.009549872
id3219 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id3263 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id3267 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id3305 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id3323 10 10 0.5000000 0.7028379 0.5803635 -0.682583120
id3330 10 10 0.7000000 0.7028379 0.6633935 -0.009549872
id3354 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id3368 10 10 0.7000000 0.7028379 0.3739278 -0.009549872
id3371 10 10 1.0000000 0.7028379 0.5611040 1.000000000
id3374 9 9 0.4444444 0.7235764 13.2344709 -1.009797928
id3398 10 10 0.6000000 0.7028379 0.1832190 -0.346066496
id3400 9 9 0.5555556 0.7103816 0.4166976 -0.534586535
id3417 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id3460 4 4 1.0000000 0.8107146 0.1626118 1.000000000
id3465 10 10 0.7000000 0.7028379 0.5689556 -0.009549872
id3521 9 9 0.8888889 0.7208560 0.4163164 0.601957778
id3573 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id3593 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id3630 10 10 0.7000000 0.7028379 0.9258058 -0.009549872
id3635 10 10 0.5000000 0.7028379 0.3598517 -0.682583120
id3641 9 9 0.7777778 0.7103816 0.3912222 0.232706732
id3657 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id3692 10 10 0.7000000 0.7028379 0.5689556 -0.009549872
id3701 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id3709 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id3735 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id3809 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id3820 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id3823 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id3828 9 9 0.6666667 0.7180257 0.1290626 -0.182140726
id3831 10 10 1.0000000 0.7028379 0.6208013 1.000000000
id3847 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id3857 10 10 0.7000000 0.7028379 0.5689556 -0.009549872
id3933 10 10 1.0000000 0.7028379 0.6208013 1.000000000
id3934 10 10 1.0000000 0.7028379 0.5611040 1.000000000
id3942 10 10 0.5000000 0.7028379 0.7850652 -0.682583120
id3957 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id3970 10 10 0.6000000 0.7028379 0.2238108 -0.346066496
id3983 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4008 10 10 0.7000000 0.7028379 0.9258058 -0.009549872
id4024 10 10 1.0000000 0.7028379 1.7025164 1.000000000
id4031 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id4067 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id4097 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id4225 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id4229 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4233 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id4254 10 10 1.0000000 0.7028379 0.5116720 1.000000000
id4259 10 10 1.0000000 0.7028379 0.5611040 1.000000000
id4261 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4284 10 10 0.9000000 0.7028379 0.4300924 0.663483376
id4287 10 10 0.9000000 0.7028379 0.9390481 0.663483376
id4288 10 10 0.9000000 0.7028379 0.9390481 0.663483376
id4309 10 10 0.5000000 0.7028379 0.5803635 -0.682583120
id4328 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id4337 10 10 1.0000000 0.7028379 0.6208013 1.000000000
id4363 10 10 1.0000000 0.7028379 1.7025164 1.000000000
id4380 10 10 0.7000000 0.7028379 0.6633935 -0.009549872
id4395 9 9 0.4444444 0.7180257 0.5931586 -0.970234543
id4416 10 10 0.9000000 0.7028379 0.9390481 0.663483376
id4446 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4449 8 8 1.0000000 0.7315950 0.6055061 1.000000000
id4512 10 10 0.6000000 0.7028379 11.9895480 -0.346066496
id4552 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id4554 10 10 0.9000000 0.7028379 0.5249337 0.663483376
id4561 10 10 0.9000000 0.7028379 0.9390481 0.663483376
id4606 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id4629 10 10 0.5000000 0.7028379 0.5803635 -0.682583120
id4645 10 10 0.5000000 0.7028379 0.5094701 -0.682583120
id4652 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4673 10 10 0.7000000 0.7028379 0.3953192 -0.009549872
id4675 9 9 0.4444444 0.6863037 0.1422416 -0.770997855
id4689 10 10 0.6000000 0.7028379 0.2024194 -0.346066496
id4705 8 8 0.7500000 0.7433213 0.8147125 0.026019721
id4710 10 10 0.8000000 0.7028379 0.3239595 0.326966752
id4717 10 10 1.0000000 0.7028379 0.5713693 1.000000000
id4734 10 10 1.0000000 0.7028379 0.5713693 1.000000000
id4751 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4756 10 10 0.7000000 0.7028379 0.8454440 -0.009549872
id4781 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id4798 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id4806 10 10 0.9000000 0.7028379 0.9390481 0.663483376
id4807 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4812 10 10 1.0000000 0.7028379 3.1266941 1.000000000
id4834 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4842 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id4883 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id4904 9 9 0.6666667 0.7235764 0.2235043 -0.205878757
id4934 10 10 0.7000000 0.7028379 0.5689556 -0.009549872
id4959 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id4961 10 10 1.0000000 0.7028379 0.5713693 1.000000000
id5014 10 10 0.5000000 0.7028379 0.3598517 -0.682583120
id5055 10 10 0.8000000 0.7028379 0.3239595 0.326966752
id5078 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id5150 10 10 0.5000000 0.7028379 0.3598517 -0.682583120
id5263 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id5274 10 10 0.7000000 0.7028379 0.6633935 -0.009549872
id5275 10 10 0.5000000 0.7028379 0.1581747 -0.682583120
id5324 10 10 0.7000000 0.7028379 0.9258058 -0.009549872
id5385 10 10 0.7000000 0.7028379 0.9258058 -0.009549872
id5398 10 10 0.6000000 0.7028379 0.1832190 -0.346066496
id5407 10 10 0.6000000 0.7028379 0.2238108 -0.346066496
id5444 10 10 1.0000000 0.7028379 0.7801840 1.000000000
id5454 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id5495 9 9 0.7777778 0.6702937 0.4260476 0.325999537
id5496 10 10 1.0000000 0.7028379 0.5116720 1.000000000
id5517 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id5522 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id5598 10 10 0.8000000 0.7028379 0.3686705 0.326966752
id5627 10 10 0.7000000 0.7028379 0.6633935 -0.009549872
id5672 10 10 0.6000000 0.7028379 0.1832190 -0.346066496
id5736 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id5739 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id5764 10 10 0.7000000 0.7028379 0.4036195 -0.009549872
id5770 10 10 0.7000000 0.7028379 0.6633935 -0.009549872
id5844 9 9 0.5555556 0.7103816 0.6036134 -0.534586535
id5853 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id5890 10 10 0.7000000 0.7028379 0.6633935 -0.009549872
id5912 10 10 0.5000000 0.7028379 0.5803635 -0.682583120
id5926 10 10 0.6000000 0.7028379 0.2046103 -0.346066496
id5966 10 10 0.8000000 0.7028379 0.3192386 0.326966752
id5969 10 10 0.9000000 0.7028379 0.5399210 0.663483376
id5989 10 10 0.6000000 0.7028379 1.3037499 -0.346066496
id5991 10 10 0.6000000 0.7028379 0.2238108 -0.346066496
id6002 10 10 0.6000000 0.7028379 0.1315260 -0.346066496
id6009 10 10 0.8000000 0.7028379 0.3686705 0.326966752
id6011 10 10 0.9000000 0.7028379 0.9390481 0.663483376
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