Residualize the genotype matrix against the per-context phenotype covariates and the genotype covariates, optionally subsetting variants to those falling within a trait's cis-window or an explicit region.
Usage
getResidualizedGenotypes(x, ...)
# S4 method for class 'QtlDataset'
getResidualizedGenotypes(
x,
contexts,
traitId = NULL,
region = NULL,
cisWindow = NULL,
samples = NULL,
phenotypeCovariatesToResidualize = NULL,
genotypeCovariatesToResidualize = NULL,
residualizePhenotypeCovariates = TRUE,
residualizeGenotypeCovariates = TRUE,
residualizePhenotypeCovariatesFromGenotypes = NULL,
residualizeGenotypeCovariatesFromGenotypes = NULL,
covariateNaAction = c("impute", "drop"),
...
)Arguments
- x
A
QtlDatasetobject.- ...
Selection arguments:
traitId,region,cisWindow,phenotypeCovariatesToRemove,genotypeCovariatesToRemove, andcovariateNaAction("impute", the default, mean-imputes missing covariate cells;"drop"removes samples with any missing covariate).- contexts
Character vector. Context(s) whose data to extract.
- traitId
Character or
NULL. Molecular trait / feature identifier to select;NULLmatches all traits in the dataset.- region
Character (length 1,
"chr:start-end") orNULL. Restrict variants to this region;NULLuses the full cis window / all regions.- cisWindow
Integer or
NULL. Half-width (bp) of the cis window around the trait;NULLuses the dataset default.- samples
Character vector or
NULL. Restrict to these sample IDs;NULLuses all samples.- phenotypeCovariatesToResidualize
Character vector or
NULL. Phenotype covariate names to residualize;NULLuses the dataset default set.- genotypeCovariatesToResidualize
Character vector or
NULL. Genotype covariate names to residualize;NULLuses the dataset default set.- residualizePhenotypeCovariates
Logical. Whether to residualize the phenotype covariates. Default
TRUE.- residualizeGenotypeCovariates
Logical. Whether to residualize the genotype covariates. Default
TRUE.- residualizePhenotypeCovariatesFromGenotypes
Logical or
NULL. Whether to residualize phenotype covariates out of the genotype design;NULLuses the default.- residualizeGenotypeCovariatesFromGenotypes
Logical or
NULL. Whether to residualize genotype covariates out of the genotype design;NULLuses the default.- covariateNaAction
Character. How to handle missing covariate values.
Examples
data(qtlDatasetExample)
getResidualizedGenotypes(qtlDatasetExample, contexts = "brain")
#> chr22:14560203:A:G chr22:14564328:T:C chr22:14850625:T:G
#> NA06989 -0.5390082 -0.6824555 1.7101739
#> NA11891 2.4925545 1.3013034 -0.5860761
#> NA11843 -0.5152018 1.3532562 -0.5631626
#> NA12341 -0.3199575 -0.7607918 -0.5944045
#> NA12739 2.2470156 1.4431574 -0.5875487
#> NA10850 -0.3297108 -0.7374038 1.6880729
#> NA06984 2.2570804 -0.6737760 1.7078196
#> NA12877 -0.3292517 1.3542939 -0.6004500
#> NA12275 -0.5154487 -0.7389504 1.7254984
#> NA06986 -0.3005199 1.2853960 1.7070604
#> NA12272 -0.5689368 -0.6106877 -0.5981149
#> NA10845 -0.2918757 1.2646675 -0.5761385
#> NA10852 -0.5196082 -0.7289759 -0.5660288
#> NA07051 -0.3232364 -0.7529291 -0.5965373
#> NA12400 -0.5600812 1.4608755 1.6964668
#> NA12344 -0.3038897 -0.7993217 -0.5839531
#> NA12777 -0.5519681 -0.6513779 -0.5870775
#> NA12287 -0.3121745 -0.7794551 1.6994795
#> NA10837 -0.5409384 -0.6778267 -0.5799032
#> NA12383 -0.2907950 -0.8307224 -0.5754355
#> NA12340 -0.5172047 -0.7347394 1.7243562
#> NA12708 -0.2999039 -0.8088795 -0.5813605
#> NA12273 -0.5383437 -0.6840489 -0.5782154
#> NA11892 -0.3050059 -0.7966451 1.7041424
#> NA12546 -0.5188649 -0.7307584 -0.5655453
#> NA12843 -0.3289011 -0.7393453 -0.6002220
#> NA12766 -0.5386003 -0.6834335 -0.5783823
#> NA12348 -0.2845842 -0.8456158 -0.5713956
#> NA12817 -0.5680371 -0.6128450 1.6912918
#> NA10840 -0.2846238 1.2472776 -0.5714214
#> NA06997 -0.5574432 1.4545497 1.6981827
#> NA11917 -0.3286787 -0.7398787 -0.6000773
#> NA12718 -0.5272988 -0.7105340 -0.5710312
#> NA12282 -0.3055666 -0.7953006 -0.5850439
#> NA11920 -0.5426622 -0.6736933 -0.5810244
#> NA12776 -0.2929703 -0.8255061 1.7119711
#> NA12283 -0.5545053 -0.6452939 -0.5887279
#> NA07435 -0.3237670 1.3411417 -0.5968824
#> NA12828 -0.5590212 -0.6344648 1.6971563
#> NA07045 -0.2886821 1.2570094 -0.5740612
#> NA07031 -0.5411759 -0.6772573 -0.5800576
#> NA12336 -0.2902171 1.2606902 -0.5750596
#> NA07349 -0.5619146 1.4652719 -0.5935473
#> NA12827 -0.3064423 1.2995977 1.7032081
#> NA12375 -0.5377893 1.4074203 -0.5778548
#> NA12343 -0.2921695 -0.8274264 -0.5763296
#> NA12335 -0.5616204 -0.6282320 1.6954656
#> NA12778 -0.2978361 -0.8138380 -0.5800155
#> NA12832 -0.5562231 -0.6411746 -0.5898452
#> NA11930 -0.2832795 1.2440542 1.7182745
#> NA12890 -0.5650506 -0.6200066 -0.5955872
#> NA07037 2.4856809 1.3177859 -0.5905471
#> NA07347 -0.5511356 -0.6533743 1.7022855
#> NA12829 -0.3328289 1.3628720 -0.6027769
#> NA12749 2.2796076 -0.7277955 -0.5663490
#> NA11894 -0.3165484 -0.7689667 -0.5921870
#> NA12286 -0.5299034 1.3885101 1.7160962
#> NA10865 2.4773996 1.3376443 -0.5959338
#> NA10864 2.2638672 -0.6900505 -0.5765874
#> NA10853 -0.3183278 -0.7646998 1.6954771
#> NA11918 -0.5172687 -0.7345860 1.7243146
#> NA12830 -0.3034106 1.2923278 1.7051801
#> NA12818 -0.5512896 1.4397936 -0.5866362
#> NA10836 -0.3058642 -0.7945870 -0.5852374
#> NA11893 2.2727075 -0.7112494 -0.5708372
#> NA11919 -0.2844774 -0.8458717 -0.5713262
#> NA12489 2.2670753 1.3950551 -0.5745007
#> NA12399 -0.3182482 -0.7648906 -0.5932927
#> NA12413 -0.5202890 -0.7273435 -0.5664716
#> NA10843 -0.2912325 -0.8296732 -0.5757201
#> NA12842 2.2857325 1.3503158 -0.5623650
#> NA12347 -0.2869459 -0.8399525 -0.5729318
#> NA07346 2.2358157 1.4700144 -0.5948337
#> NA12775 -0.2969542 -0.8159529 -0.5794418
#> NA07014 -0.5658511 -0.6180869 -0.5961079
#> NA12767 -0.3324683 -0.7307913 -0.6025423
#> NA12889 -0.5694100 1.4832455 -0.5984227
#> NA12386 -0.3184305 1.3283449 -0.5934113
#> NA06995 -0.5399720 -0.6801442 -0.5792746
#> NA12376 -0.3108278 1.3101141 -0.5884661
#> NA12342 -0.5208741 1.3668580 -0.5668521
#> NA12748 2.4621661 1.3741736 -0.6058425
#> NA11931 -0.5257254 1.3784914 -0.5700077
#> NA12045 -0.3104562 -0.7835756 -0.5882243
#> NA12750 2.2367491 -0.6250223 -0.5942266
#> NA11831 -0.2895597 -0.8336847 1.7141895
#> NA12146 -0.5507335 -0.6543385 -0.5862745
#> NA11882 -0.3082434 -0.7888818 1.7020366
#> NA07056 -0.5468444 1.4291341 -0.5837448
#> NA12707 -0.3221996 -0.7554153 -0.5958629
#> NA12154 2.2751201 -0.7170346 -0.5692679
#> NA12753 -0.3347377 -0.7253494 -0.6040184
#> NA11839 -0.5320498 -0.6991414 -0.5741215
#> NA10859 -0.3358869 -0.7225935 1.6840556
#> NA12875 -0.5265131 1.3803802 1.7183015
#> NA07348 -0.3106358 -0.7831449 -0.5883412
#> NA12156 -0.5205484 1.3660771 1.7221813
#> NA12044 -0.2955801 -0.8192481 -0.5785480
#> NA11992 -0.5272188 -0.7107261 -0.5709791
#> NA11829 -0.3211981 -0.7578168 -0.5952115
#> NA12239 -0.5318296 -0.6996695 -0.5739782
#> NA12762 -0.2917421 1.2643470 -0.5760515
#> NA12716 -0.5638789 -0.6228162 1.6939965
#> NA12878 -0.2838165 -0.8474567 -0.5708963
#> NA10856 -0.5587364 -0.6351479 -0.5914800
#> NA12874 -0.3059555 -0.7943682 -0.5852968
#> NA12760 2.2709674 -0.7070765 -0.5719691
#> NA06985 2.5182776 -0.8531784 -0.5693443
#> NA12003 -0.5246332 -0.7169261 -0.5692973
#> NA10835 -0.3098167 1.3076893 1.7010132
#> NA07022 -0.5146002 1.3518136 1.7260503
#> NA12813 -0.3027099 1.2906475 -0.5831857
#> NA10839 -0.5348308 -0.6924727 -0.5759304
#> NA07055 -0.3024253 -0.8028335 -0.5830005
#> NA12056 -0.5263057 1.3798829 -0.5703852
#> NA10863 -0.2937337 -0.8236755 -0.5773470
#> NA12145 -0.5448516 -0.6684432 -0.5824485
#> NA12814 -0.3081020 -0.7892209 -0.5866930
#> NA10847 -0.5550037 -0.6440988 -0.5890520
#> NA12006 -0.3190787 1.3298994 -0.5938329
#> NA12763 -0.5203913 -0.7270980 -0.5665381
#> NA07357 -0.3212733 -0.7576366 -0.5952604
#> NA12144 -0.5542935 1.4469967 1.7002315
#> NA10831 -0.3023528 1.2897912 1.7058681
#> NA07000 -0.5556068 1.4501460 -0.5894444
#> NA11832 -0.2807055 1.2378817 -0.5688727
#> NA06991 -0.5424878 -0.6741114 -0.5809110
#> NA11840 -0.3332539 -0.7289074 1.6857683
#> NA12802 -0.5185635 -0.7314812 -0.5653492
#> NA12761 2.4781460 -0.7569440 1.6933733
#> NA10830 2.2537311 -0.6657446 -0.5831805
#> NA10855 -0.2926596 -0.8262511 1.7121731
#> NA06994 -0.5235766 -0.7194598 1.7202115
#> NA11993 -0.3129961 1.3153134 1.6989451
#> NA11995 -0.5252806 -0.7153738 -0.5697184
#> NA12891 -0.3073880 -0.7909330 -0.5862286
#> NA12864 2.2833656 1.3559914 -0.5639045
#> NA12751 -0.3014256 1.2875677 -0.5823503
#> NA10861 2.2617210 -0.6849040 -0.5779834
#> NA12005 -0.2990831 -0.8108478 -0.5808266
#> NA12234 -0.5300954 -0.7038280 -0.5728502
#> NA07345 -0.3164021 1.3234809 -0.5920919
#> NA07029 -0.5497786 1.4361700 -0.5856533
#> NA12892 -0.2812204 -0.8536819 -0.5692077
#> NA12248 -0.5349880 -0.6920958 1.7127889
#> NA10846 -0.3094524 1.3068160 1.7012501
#> NA12801 -0.5571426 -0.6389697 -0.5904433
#> NA12872 2.5008655 -0.8114246 1.7081514
#> NA12155 -0.5343209 -0.6936953 -0.5755988
#> NA06993 -0.3098241 -0.7850913 -0.5878132
#> NA11830 -0.5362127 -0.6891588 -0.5768293
#> NA10838 -0.3102819 -0.7839936 -0.5881109
#> NA12249 -0.5238509 1.3739965 1.7200331
#> NA12057 2.4730009 -0.7446064 -0.5987949
#> NA12812 -0.5515383 1.4403899 -0.5867980
#> NA11881 -0.3029427 1.2912057 -0.5833371
#> NA11994 2.2415478 -0.6365295 -0.5911053
#> NA12873 2.5091238 1.2615707 -0.5752985
#> NA12815 -0.5190045 1.3623749 -0.5656361
#> NA12740 -0.3077535 1.3027418 -0.5864663
#> NA12752 2.2482172 -0.6525224 -0.5867671
#> NA12043 -0.3208116 1.3340548 -0.5949601
#> NA12264 -0.5562035 -0.6412217 -0.5898325
#> NA10854 -0.3109067 -0.7824954 1.7003042
#> NA12865 -0.5397418 1.4121022 1.7096967
#> chr22:14870204:T:C chr22:14878387:G:A chr22:14880040:A:G
#> NA06989 -1.1203164 -0.68257727 -0.7383081
#> NA11891 0.5338131 -0.65761938 1.2216989
#> NA11843 -1.0035818 -0.69501078 -0.7950967
#> NA12341 0.4710290 3.39362516 -0.4461483
#> NA12739 1.7272376 -0.67543028 2.6911153
#> NA10850 0.4232038 1.37644039 1.2755077
#> NA06984 0.3192627 -0.68068687 0.9687162
#> NA12877 0.4254548 -0.64607805 -0.4239775
#> NA12275 -1.0047921 1.32739681 -0.7945079
#> NA06986 -0.8909860 1.36119466 -0.4925156
#> NA12272 1.6475833 -0.66694623 -0.6669151
#> NA10845 -0.8485991 1.35668000 -0.5131358
#> NA10852 -1.0251886 1.32956926 -0.7845855
#> NA07051 0.4549509 -0.64921969 -0.4383266
#> NA12400 0.2336791 1.35070739 -0.6880395
#> NA12344 -0.9075100 -0.65932402 -0.4844770
#> NA12777 0.2734617 1.34647011 -0.7073928
#> NA12287 -0.9481346 1.36728161 -0.4647141
#> NA10837 0.3275459 -0.68156913 -0.7337035
#> NA12383 0.6140276 1.35611558 1.1826765
#> NA12340 -1.0134029 -0.69396472 -0.7903190
#> NA12708 -0.8879657 -0.66140571 -0.4939849
#> NA12273 -1.1170582 -0.68292431 -0.7398932
#> NA11892 -0.9129833 1.36353762 -0.4818144
#> NA12546 -1.0215437 -0.69309764 -0.7863587
#> NA12843 -1.0301535 -0.64626116 -0.4248139
#> NA12766 -1.1183166 -0.68279027 -0.7392810
#> NA12348 0.6444826 -0.66940688 1.1678608
#> NA12817 0.1946672 1.35486259 -0.6690611
#> NA10840 -0.8130392 1.35289248 -0.5304348
#> NA06997 -1.2107131 1.34932964 -0.6943323
#> NA11917 -1.0290629 -0.64637732 -0.4253444
#> NA12718 0.3944278 1.33358590 -0.7662400
#> NA12282 0.5415948 -0.65844822 1.2179133
#> NA11920 0.3190936 -0.68066886 -0.7295916
#> NA12776 -0.8539666 -0.66502698 -0.5105246
#> NA12283 -1.1963068 -0.67448346 -0.7013406
#> NA07435 0.4523493 -0.64894260 1.2613291
#> NA12828 0.2388768 -0.67212489 1.0078221
#> NA07045 -0.8329394 -0.66726661 -0.5207539
#> NA07031 -1.1309460 3.36311225 -0.7331371
#> NA12336 -0.8404660 -0.66646494 -0.5170923
#> NA07349 -1.2326385 -0.67061375 -0.6836661
#> NA12827 0.5373009 0.01196648 -0.4783880
#> NA12375 0.3429876 -0.68321383 0.9571747
#> NA12343 -0.8500398 -0.66544523 -0.5124349
#> NA12335 -1.2311960 1.35151128 -0.6843678
#> NA12778 0.5795014 1.35979299 -0.4989175
#> NA12832 0.2525974 -0.67358629 1.0011473
#> NA11930 -0.8064477 -0.67008826 -0.5336414
#> NA12890 0.2093116 -0.66897588 1.0222049
#> NA07037 0.5001085 1.36824920 1.2380954
#> NA07347 -1.1797836 -0.67624337 -0.7093788
#> NA12829 -1.0494137 -0.64420973 -0.4154442
#> NA12749 1.8870526 -0.69245232 2.6133691
#> NA11894 0.4877457 -0.65271270 1.2441096
#> NA12286 -1.0756713 1.33494621 -0.7600269
#> NA10865 0.4595009 -0.64970432 1.2578500
#> NA10864 1.8098695 -0.68423147 2.6509168
#> NA10853 -0.9783071 -0.65178336 -0.4500359
#> NA11918 -1.0137166 -0.69393131 -0.7901664
#> NA12830 0.5521669 -0.65957426 -0.4856200
#> NA12818 0.2767887 -0.67616293 -0.7090113
#> NA10836 0.5401357 1.36398587 -0.4797670
#> NA11893 1.8532181 -0.68884858 2.6298288
#> NA11919 0.6450059 1.35281605 1.1676062
#> NA12489 1.8256003 1.33637170 2.6432642
#> NA12399 0.4794105 -0.65182491 2.9465546
#> NA12413 0.4288008 -0.69235387 0.9154286
#> NA10843 0.6118822 -0.66593459 -0.5146700
#> NA12842 1.9170860 1.32662747 2.5987585
#> NA12347 0.6329019 1.35410526 -0.5248956
#> NA07346 0.2149913 -0.66958083 1.0194418
#> NA12775 -0.8735016 -0.66294629 -0.5010213
#> NA07014 0.2053862 1.35372089 -0.6742757
#> NA12767 0.4096823 1.37788058 -0.4163046
#> NA12889 1.6452629 1.35557959 -0.6657863
#> NA12386 1.9358444 1.37054895 1.2485992
#> NA06995 0.3322849 -0.68207387 0.9623813
#> NA12376 0.5157964 1.36657827 1.2304636
#> NA12342 -1.0313957 -0.69204830 -0.7815659
#> NA12748 0.3848035 -0.64174823 1.2941885
#> NA11931 -1.0551843 1.33276412 -0.7699933
#> NA12045 -0.9397086 -0.65589452 -0.4688132
#> NA12750 0.2195680 -0.67006830 1.0172153
#> NA11831 -0.8372424 1.35547039 -0.5186605
#> NA12146 0.2795157 1.34582530 -0.7103379
#> NA11882 -0.9288583 -0.65705020 -0.4740916
#> NA07056 -1.1587417 -0.67848456 -0.7196151
#> NA12707 -0.9972926 -0.64976121 -0.4407999
#> NA12154 1.8650481 1.33217007 2.6240737
#> NA12753 -1.0587732 1.37906583 -0.4108911
#> NA11839 0.3711315 1.33606721 -0.7549068
#> NA10859 -1.0644086 -0.64261261 -0.4081496
#> NA12875 0.3982809 1.33317551 -0.7681144
#> NA07348 1.9740656 1.36647797 -0.4683847
#> NA12156 -1.0297987 -0.69221839 -0.7823428
#> NA12044 0.5905641 -0.66366398 -0.5042993
#> NA11992 -1.0625070 -0.68873460 -0.7664310
#> NA11829 0.4649456 1.37199443 -0.4431889
#> NA12239 -1.0851161 -0.68632649 -0.7554322
#> NA12762 -0.8479437 1.35661019 -0.5134546
#> NA12716 -1.2422706 -0.66958782 -0.6789803
#> NA12878 0.6482470 1.35247084 -0.5323606
#> NA10856 -1.2170540 1.35000501 -0.6912476
#> NA12874 0.5396881 -0.65824514 -0.4795493
#> NA12760 1.8446852 -0.68793972 0.9355897
#> NA06985 2.1172744 1.35122467 1.1603378
#> NA12003 -1.0498287 -0.69008498 -0.7725987
#> NA10835 -0.9365728 -0.65622852 -0.4703387
#> NA07022 0.4566957 1.32695369 -0.7965318
#> NA12813 -0.9017246 -0.65994024 -0.4872915
#> NA10839 0.3574950 -0.68475903 -0.7482730
#> NA07055 0.5569986 -0.66008889 -0.4879704
#> NA12056 1.8566254 -0.68921148 0.9297811
#> NA10863 2.0569452 -0.66462828 -0.5087036
#> NA12145 -1.1489697 -0.67952538 -0.7243690
#> NA12814 -0.9281648 -0.65712406 -0.4744290
#> NA10847 0.2585769 -0.67422318 -0.7001517
#> NA12006 1.9326657 -0.65139116 -0.4482446
#> NA12763 -1.0290286 -0.69230042 -0.7827175
#> NA07357 1.9219047 -0.65024500 1.2553806
#> NA12144 -1.1952682 -0.67459409 -0.7018458
#> NA10831 -0.8999737 -0.66012673 -0.4881433
#> NA07000 -1.2017081 1.34837051 -0.6987130
#> NA11832 0.6635017 -0.67143263 -0.5397817
#> NA06991 0.3199485 -0.68075992 -0.7300075
#> NA11840 -1.0514976 -0.64398778 -0.4144305
#> NA12802 0.4372620 -0.69325508 0.9113124
#> NA12761 0.4631609 -0.65009415 1.2560695
#> NA10830 1.7601671 1.34334105 2.6750959
#> NA10855 -0.8524432 -0.66518924 -0.5112657
#> NA06994 0.4126799 -0.69063682 0.9232710
#> NA11993 -0.9521630 -0.65456799 -0.4627544
#> NA11995 0.4043245 -0.68974688 -0.7710544
#> NA12891 0.5326637 1.36478172 -0.4761321
#> NA12864 1.9054802 -0.69441505 2.6044045
#> NA12751 -0.8954269 -0.66061100 -0.4903552
#> NA10861 0.3420180 -0.68311056 0.9576463
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#> chr22:15645194:G:A chr22:15647006:T:C chr22:15648016:C:T
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#> chr22:15695458:G:T chr22:15695503:A:G chr22:15696313:T:C
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#> NA11930 -0.53219808 1.465670e+00 1.488825163
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#> NA07022 -0.63787249 2.556172e-01 0.260170497
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#> chr22:15706432:C:T chr22:15706668:G:A chr22:15707595:T:C
#> NA06989 -0.6579759 0.8539626 0.8896580
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#> chr22:15708627:C:T chr22:15709601:T:G chr22:15711656:C:T
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#> chr22:15719003:A:G chr22:15719068:C:T chr22:15719404:A:G
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#> chr22:15774989:T:C chr22:15775610:G:A chr22:15776459:C:T
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#> chr22:15776612:C:T chr22:15777875:T:C chr22:15778508:T:C
#> NA06989 -0.7399590 -0.7398574 0.2548381
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#> NA12865 2.4877728 2.4874961 1.6800872
#> chr22:15778800:C:T chr22:15778812:A:G chr22:15779211:A:C
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#> chr22:15783936:G:C chr22:15784605:A:G chr22:15785173:C:T
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#> NA12865 -0.9761913 -1.11726590 -0.5906305423
#> chr22:15787349:C:T chr22:15787566:C:T chr22:15787755:T:C
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#> chr22:15789897:G:A chr22:15789957:G:C chr22:15790373:A:G
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#> chr22:15790790:G:A chr22:15791899:A:G chr22:15792216:A:G
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#> chr22:15792806:T:C chr22:15794103:T:C chr22:15794640:G:A
#> NA06989 0.6953921 -0.0134017 0.6564332
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#> chr22:15816846:G:A chr22:15817310:C:T chr22:15821524:A:G
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#> chr22:15826914:T:G chr22:15826991:T:C
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