HWETest.RdTest experiment features for Hardy Weinberg equilibrium.
HWETest(
object,
experiment = c("hla_alleles", "hla_aa", "hla_g_groups", "hla_supertypes",
"hla_NK_ligands"),
HWE_group = NULL,
HWE_cutoff = NULL,
as.MiDAS = FALSE
)MiDAS object.
String specifying experiment to test. Valid values
includes "hla_alleles", "hla_aa", "hla_g_groups",
"hla_supertypes", "hla_NK_ligands".
Expression defining samples grouping to test for Hardy Weinberg equilibrium. By default samples are not grouped.
Number specifying p-value threshold. When HWE_group
is specified both groups are thresholded.
Logical flag indicating if MiDAS object should be returned.
Data frame with Hardy Weinberg Equilibrium test results or a filtered MiDAS object.
Setting as.MiDAS to TRUE will filter MiDAS object based on
p-value cut-off given by HWE_cutoff.
# create MiDAS object
midas <- prepareMiDAS(hla_calls = MiDAS_tut_HLA,
colData = MiDAS_tut_pheno,
experiment = "hla_alleles"
)
# get HWE p-values as data frame
HWETest(midas, experiment = "hla_alleles")
#> var p.value
#> 1 A*01:01 9.815768e-01
#> 2 A*01:02 9.747476e-01
#> 3 A*01:234 9.873786e-01
#> 4 A*01:237 9.873786e-01
#> 5 A*01:274 9.494700e-01
#> 6 A*01:43 9.873786e-01
#> 7 A*01:98 9.873786e-01
#> 8 A*02:01 9.932791e-01
#> 9 A*02:02 9.747476e-01
#> 10 A*02:03 9.115621e-01
#> 11 A*02:05 4.993169e-04
#> 12 A*02:06 4.712638e-08
#> 13 A*02:07 9.115621e-01
#> 14 A*02:08 9.747476e-01
#> 15 A*02:10 9.621104e-01
#> 16 A*02:211 9.873786e-01
#> 17 A*02:22 9.873786e-01
#> 18 A*02:324 9.873786e-01
#> 19 A*02:60 9.873786e-01
#> 20 A*02:614 9.873786e-01
#> 21 A*02:642 9.873786e-01
#> 22 A*02:686 9.873786e-01
#> 23 A*02:753 9.873786e-01
#> 24 A*02:763 9.873786e-01
#> 25 A*03:01 5.024356e-01
#> 26 A*03:02 8.360935e-01
#> 27 A*03:205 9.873786e-01
#> 28 A*03:24 9.873786e-01
#> 29 A*03:312 9.621104e-01
#> 30 A*03:72 9.747476e-01
#> 31 A*11:01 1.055618e-01
#> 32 A*11:02 9.873786e-01
#> 33 A*11:03 9.873786e-01
#> 34 A*11:12 9.873786e-01
#> 35 A*11:306 9.621104e-01
#> 36 A*11:43 9.873786e-01
#> 37 A*11:50Q 9.873786e-01
#> 38 A*11:88 9.621104e-01
#> 39 A*23:01 4.466456e-01
#> 40 A*23:17 9.873786e-01
#> 41 A*23:18 9.873786e-01
#> 42 A*24:02 7.551682e-01
#> 43 A*24:03 9.747476e-01
#> 44 A*24:04 9.873786e-01
#> 45 A*24:07 1.795833e-219
#> 46 A*24:104 9.747476e-01
#> 47 A*24:20 9.494700e-01
#> 48 A*24:50 9.494700e-01
#> 49 A*24:95 9.873786e-01
#> 50 A*25:01 3.985913e-01
#> 51 A*25:09 9.747476e-01
#> 52 A*25:25 9.873786e-01
#> 53 A*26:01 9.853229e-01
#> 54 A*26:02 9.494700e-01
#> 55 A*26:03 9.747476e-01
#> 56 A*26:08 9.621104e-01
#> 57 A*26:16 9.873786e-01
#> 58 A*29:01 9.241927e-01
#> 59 A*29:02 4.777554e-01
#> 60 A*29:119 9.621104e-01
#> 61 A*30:01 5.511430e-01
#> 62 A*30:02 4.482222e-01
#> 63 A*30:04 9.621104e-01
#> 64 A*31:01 3.449400e-01
#> 65 A*31:08 9.873786e-01
#> 66 A*31:21 9.873786e-01
#> 67 A*32:01 3.449400e-01
#> 68 A*32:02 9.873786e-01
#> 69 A*32:116 9.494700e-01
#> 70 A*33:01 7.494065e-01
#> 71 A*33:03 7.987058e-01
#> 72 A*33:05 9.747476e-01
#> 73 A*33:125 9.873786e-01
#> 74 A*33:163 9.873786e-01
#> 75 A*33:51 9.873786e-01
#> 76 A*34:01 9.873786e-01
#> 77 A*34:02 9.241927e-01
#> 78 A*66:01 8.737410e-01
#> 79 A*68:01 7.151258e-01
#> 80 A*68:02 7.372008e-01
#> 81 A*68:04 9.873786e-01
#> 82 A*68:16 9.873786e-01
#> 83 A*68:164 9.873786e-01
#> 84 A*68:17 9.873786e-01
#> 85 A*68:23 9.873786e-01
#> 86 A*68:66 9.873786e-01
#> 87 A*69:01 9.241927e-01
#> 88 A*74:01 9.747476e-01
#> 89 B*07:02 5.715522e-02
#> 90 B*07:04 9.873786e-01
#> 91 B*07:05 9.368297e-01
#> 92 B*07:06 9.368297e-01
#> 93 B*07:10 9.873786e-01
#> 94 B*07:14 9.873786e-01
#> 95 B*07:22 9.873786e-01
#> 96 B*07:47 9.873786e-01
#> 97 B*08:01 3.148466e-01
#> 98 B*08:156 9.747476e-01
#> 99 B*08:94 9.873786e-01
#> 100 B*13:01 9.368297e-01
#> 101 B*13:02 1.954175e-02
#> 102 B*13:117 9.873786e-01
#> 103 B*14:01 7.250487e-01
#> 104 B*14:02 5.186921e-01
#> 105 B*14:28 9.873786e-01
#> 106 B*15:01 1.423391e-03
#> 107 B*15:02 9.241927e-01
#> 108 B*15:03 8.989411e-01
#> 109 B*15:07 9.747476e-01
#> 110 B*15:09 9.747476e-01
#> 111 B*15:10 9.494700e-01
#> 112 B*15:11 9.621104e-01
#> 113 B*15:12 9.873786e-01
#> 114 B*15:15 9.873786e-01
#> 115 B*15:17 8.737410e-01
#> 116 B*15:18 9.621104e-01
#> 117 B*15:20 9.873786e-01
#> 118 B*15:212 9.873786e-01
#> 119 B*15:220 9.873786e-01
#> 120 B*15:25 9.621104e-01
#> 121 B*15:256 9.873786e-01
#> 122 B*15:27 9.873786e-01
#> 123 B*15:39 9.873786e-01
#> 124 B*15:63 9.873786e-01
#> 125 B*18:01 1.366843e-01
#> 126 B*18:02 9.873786e-01
#> 127 B*18:03 9.873786e-01
#> 128 B*18:07 9.873786e-01
#> 129 B*27:02 8.863330e-01
#> 130 B*27:03 9.621104e-01
#> 131 B*27:04 9.747476e-01
#> 132 B*27:05 1.865273e-02
#> 133 B*27:06 9.873786e-01
#> 134 B*27:127 9.747476e-01
#> 135 B*27:14 9.873786e-01
#> 136 B*35:01 7.885904e-02
#> 137 B*35:02 1.515212e-05
#> 138 B*35:03 5.294094e-01
#> 139 B*35:05 1.795833e-219
#> 140 B*35:08 8.111342e-01
#> 141 B*35:09 9.873786e-01
#> 142 B*35:17 9.873786e-01
#> 143 B*35:194 9.873786e-01
#> 144 B*35:41 9.873786e-01
#> 145 B*35:42 9.873786e-01
#> 146 B*35:43 9.873786e-01
#> 147 B*35:60 9.873786e-01
#> 148 B*35:67 9.873786e-01
#> 149 B*35:71 9.873786e-01
#> 150 B*37:01 6.889442e-01
#> 151 B*37:68 9.873786e-01
#> 152 B*38:01 1.116598e-01
#> 153 B*38:02 9.368297e-01
#> 154 B*39:01 6.417333e-01
#> 155 B*39:05 9.873786e-01
#> 156 B*39:06 8.737410e-01
#> 157 B*39:09 9.873786e-01
#> 158 B*40:01 8.582846e-01
#> 159 B*40:02 6.534281e-01
#> 160 B*40:06 4.993169e-04
#> 161 B*40:117 9.873786e-01
#> 162 B*40:21 9.873786e-01
#> 163 B*40:32 9.873786e-01
#> 164 B*40:353 9.873786e-01
#> 165 B*40:49 9.873786e-01
#> 166 B*41:01 8.863330e-01
#> 167 B*41:02 8.863330e-01
#> 168 B*42:01 9.368297e-01
#> 169 B*42:02 9.747476e-01
#> 170 B*44:02 7.252547e-01
#> 171 B*44:03 9.347324e-01
#> 172 B*44:04 9.873786e-01
#> 173 B*44:05 9.368297e-01
#> 174 B*44:06 9.873786e-01
#> 175 B*44:27 8.737410e-01
#> 176 B*44:270 9.747476e-01
#> 177 B*44:37 9.873786e-01
#> 178 B*44:55 9.873786e-01
#> 179 B*45:01 8.111342e-01
#> 180 B*46:01 8.611683e-01
#> 181 B*47:01 9.241927e-01
#> 182 B*47:04 9.747476e-01
#> 183 B*48:01 2.064515e-08
#> 184 B*49:01 4.189087e-01
#> 185 B*50:01 6.185757e-01
#> 186 B*50:02 9.873786e-01
#> 187 B*51:01 8.550926e-01
#> 188 B*51:02 9.873786e-01
#> 189 B*51:05 9.873786e-01
#> 190 B*51:07 9.494700e-01
#> 191 B*51:08 9.241927e-01
#> 192 B*51:09 9.873786e-01
#> 193 B*51:173Q 9.873786e-01
#> 194 B*51:203 9.873786e-01
#> 195 B*51:230 9.873786e-01
#> 196 B*52:01 4.189087e-01
#> 197 B*53:01 8.989411e-01
#> 198 B*54:01 8.486181e-01
#> 199 B*55:01 1.350792e-01
#> 200 B*55:02 8.989411e-01
#> 201 B*56:01 7.863157e-01
#> 202 B*56:03 9.873786e-01
#> 203 B*56:09 9.873786e-01
#> 204 B*57:01 7.697112e-01
#> 205 B*57:02 9.115621e-01
#> 206 B*57:03 9.241927e-01
#> 207 B*58:01 7.250487e-01
#> 208 B*58:02 9.368297e-01
#> 209 B*59:01 9.747476e-01
#> 210 B*67:01 9.873786e-01
#> 211 B*73:01 9.747476e-01
#> 212 C*01:02 7.392314e-01
#> 213 C*01:03 9.747476e-01
#> 214 C*01:103 9.873786e-01
#> 215 C*01:22 9.873786e-01
#> 216 C*01:51 9.873786e-01
#> 217 C*02:02 9.616256e-01
#> 218 C*02:06 9.873786e-01
#> 219 C*02:10 8.989411e-01
#> 220 C*02:20 9.873786e-01
#> 221 C*03:02 8.360935e-01
#> 222 C*03:03 2.887710e-01
#> 223 C*03:04 1.546051e-02
#> 224 C*03:05 9.873786e-01
#> 225 C*03:06 9.873786e-01
#> 226 C*03:344 9.494700e-01
#> 227 C*03:39 9.621104e-01
#> 228 C*03:85 9.873786e-01
#> 229 C*04:01 4.869612e-02
#> 230 C*04:03 9.621104e-01
#> 231 C*04:277 9.873786e-01
#> 232 C*05:01 1.118098e-01
#> 233 C*05:05 9.873786e-01
#> 234 C*05:37 9.873786e-01
#> 235 C*06:02 3.701502e-01
#> 236 C*06:09 9.873786e-01
#> 237 C*07:01 5.073501e-01
#> 238 C*07:02 3.290282e-01
#> 239 C*07:04 5.844583e-01
#> 240 C*07:18 8.737410e-01
#> 241 C*07:204 9.873786e-01
#> 242 C*07:51 9.747476e-01
#> 243 C*07:578 9.115621e-01
#> 244 C*07:615 9.873786e-01
#> 245 C*07:696 9.747476e-01
#> 246 C*08:01 7.250487e-01
#> 247 C*08:02 7.873761e-01
#> 248 C*08:03 4.642348e-12
#> 249 C*12:02 4.189087e-01
#> 250 C*12:03 5.768731e-02
#> 251 C*12:132 9.873786e-01
#> 252 C*12:167 9.873786e-01
#> 253 C*12:28 9.873786e-01
#> 254 C*14:02 6.417333e-01
#> 255 C*14:03 9.368297e-01
#> 256 C*15:02 4.466456e-01
#> 257 C*15:05 8.486181e-01
#> 258 C*15:07 9.873786e-01
#> 259 C*15:09 9.873786e-01
#> 260 C*16:01 4.270695e-01
#> 261 C*16:02 7.987058e-01
#> 262 C*16:04 9.494700e-01
#> 263 C*17:01 8.611683e-01
#> 264 C*17:03 8.737410e-01
#> 265 C*18:02 9.621104e-01
#> 266 DPA1*01:03 1.029139e-03
#> 267 DPA1*01:04 8.486181e-01
#> 268 DPA1*01:05 9.873786e-01
#> 269 DPA1*01:11 9.873786e-01
#> 270 DPA1*02:01 1.996524e-01
#> 271 DPA1*02:02 6.702482e-25
#> 272 DPA1*02:06 8.863330e-01
#> 273 DPA1*02:07 8.360935e-01
#> 274 DPA1*03:01 8.989411e-01
#> 275 DPA1*04:01 9.873786e-01
#> 276 DPB1*01:01 5.754677e-01
#> 277 DPB1*02:01 1.480374e-01
#> 278 DPB1*02:02 9.717136e-02
#> 279 DPB1*03:01 8.787774e-01
#> 280 DPB1*04:01 5.594016e-05
#> 281 DPB1*04:02 9.465083e-02
#> 282 DPB1*05:01 3.458069e-14
#> 283 DPB1*06:01 2.233096e-03
#> 284 DPB1*09:01 7.494065e-01
#> 285 DPB1*104:01 5.455257e-02
#> 286 DPB1*105:01 8.235979e-01
#> 287 DPB1*107:01 9.873786e-01
#> 288 DPB1*10:01 6.889442e-01
#> 289 DPB1*113:01 9.747476e-01
#> 290 DPB1*11:01 5.186921e-01
#> 291 DPB1*124:01 8.486181e-01
#> 292 DPB1*126:01 9.115621e-01
#> 293 DPB1*131:01 9.747476e-01
#> 294 DPB1*133:01 9.873786e-01
#> 295 DPB1*135:01 9.241927e-01
#> 296 DPB1*138:01 9.873786e-01
#> 297 DPB1*13:01 8.586290e-02
#> 298 DPB1*14:01 3.053515e-01
#> 299 DPB1*150:01 9.873786e-01
#> 300 DPB1*158:01 9.873786e-01
#> 301 DPB1*15:01 8.360935e-01
#> 302 DPB1*162:01 9.368297e-01
#> 303 DPB1*16:01 8.737410e-01
#> 304 DPB1*17:01 6.401594e-02
#> 305 DPB1*18:01 9.873786e-01
#> 306 DPB1*19:01 9.115621e-01
#> 307 DPB1*20:01 9.115621e-01
#> 308 DPB1*21:01 9.494700e-01
#> 309 DPB1*22:01 9.873786e-01
#> 310 DPB1*234:01 9.873786e-01
#> 311 DPB1*23:01 8.111342e-01
#> 312 DPB1*259:01 9.873786e-01
#> 313 DPB1*271:01 9.494700e-01
#> 314 DPB1*294:01 9.873786e-01
#> 315 DPB1*33:01 9.873786e-01
#> 316 DPB1*350:01 9.115621e-01
#> 317 DPB1*351:01 9.621104e-01
#> 318 DPB1*36:01 9.873786e-01
#> 319 DPB1*38:01 9.873786e-01
#> 320 DPB1*398:01 9.873786e-01
#> 321 DPB1*40:01 9.873786e-01
#> 322 DPB1*414:01 9.115621e-01
#> 323 DPB1*41:01 9.873786e-01
#> 324 DPB1*45:01 9.873786e-01
#> 325 DPB1*461:01 9.873786e-01
#> 326 DPB1*462:01 9.873786e-01
#> 327 DPB1*463:01 9.494700e-01
#> 328 DPB1*47:01 9.873786e-01
#> 329 DPB1*519:01 9.873786e-01
#> 330 DPB1*51:01 9.873786e-01
#> 331 DPB1*547:01 9.873786e-01
#> 332 DPB1*57:01 9.621104e-01
#> 333 DPB1*651:01 9.494700e-01
#> 334 DPB1*702:01 9.115621e-01
#> 335 DPB1*744:01 9.873786e-01
#> 336 DPB1*80:01 9.873786e-01
#> 337 DPB1*88:01 9.873786e-01
#> 338 DPB1*92:01 9.873786e-01
#> 339 DQA1*01:01 1.679464e-01
#> 340 DQA1*01:02 8.227547e-01
#> 341 DQA1*01:03 5.308181e-01
#> 342 DQA1*01:04 3.985913e-01
#> 343 DQA1*01:05 6.889442e-01
#> 344 DQA1*01:06 9.873786e-01
#> 345 DQA1*01:10 9.747476e-01
#> 346 DQA1*02:01 1.909432e-01
#> 347 DQA1*03:01 4.878395e-01
#> 348 DQA1*03:02 2.655992e-04
#> 349 DQA1*03:03 4.866700e-01
#> 350 DQA1*04:01 8.582846e-01
#> 351 DQA1*04:02 9.747476e-01
#> 352 DQA1*05:01 5.414476e-03
#> 353 DQA1*05:03 7.494065e-01
#> 354 DQA1*05:05 3.596649e-01
#> 355 DQA1*05:06 9.873786e-01
#> 356 DQA1*05:07 9.873786e-01
#> 357 DQA1*05:08 9.873786e-01
#> 358 DQA1*05:09 9.241927e-01
#> 359 DQA1*06:01 1.061717e-02
#> 360 DQB1*02:01 2.985525e-03
#> 361 DQB1*02:02 3.903724e-02
#> 362 DQB1*02:10 9.873786e-01
#> 363 DQB1*03:01 3.718184e-02
#> 364 DQB1*03:02 3.816382e-01
#> 365 DQB1*03:03 6.860990e-01
#> 366 DQB1*03:04 9.115621e-01
#> 367 DQB1*03:05 9.621104e-01
#> 368 DQB1*03:19 8.611683e-01
#> 369 DQB1*03:22 7.250487e-01
#> 370 DQB1*03:251 9.747476e-01
#> 371 DQB1*03:96 9.368297e-01
#> 372 DQB1*04:01 6.403459e-06
#> 373 DQB1*04:02 3.449400e-01
#> 374 DQB1*04:23 9.621104e-01
#> 375 DQB1*05:01 2.457877e-01
#> 376 DQB1*05:02 7.582602e-02
#> 377 DQB1*05:03 4.367994e-01
#> 378 DQB1*05:04 9.494700e-01
#> 379 DQB1*05:107 9.873786e-01
#> 380 DQB1*06:01 6.401594e-02
#> 381 DQB1*06:02 7.277424e-02
#> 382 DQB1*06:03 2.835501e-01
#> 383 DQB1*06:04 8.331507e-01
#> 384 DQB1*06:07 9.873786e-01
#> 385 DQB1*06:09 7.739671e-01
#> 386 DRA*01:01 1.087711e-01
#> 387 DRA*01:02 1.087711e-01
#> 388 DRB1*01:01 4.950361e-02
#> 389 DRB1*01:02 5.423947e-03
#> 390 DRB1*01:03 8.863330e-01
#> 391 DRB1*03:01 1.854270e-03
#> 392 DRB1*03:02 9.494700e-01
#> 393 DRB1*03:07 9.873786e-01
#> 394 DRB1*04:01 3.390179e-01
#> 395 DRB1*04:02 4.042862e-03
#> 396 DRB1*04:03 2.265170e-01
#> 397 DRB1*04:04 5.670464e-01
#> 398 DRB1*04:05 6.401594e-02
#> 399 DRB1*04:06 8.989411e-01
#> 400 DRB1*04:07 1.917060e-04
#> 401 DRB1*04:08 9.115621e-01
#> 402 DRB1*04:10 9.747476e-01
#> 403 DRB1*04:13 9.873786e-01
#> 404 DRB1*04:92 9.873786e-01
#> 405 DRB1*07:01 1.105835e-01
#> 406 DRB1*08:01 1.350792e-01
#> 407 DRB1*08:02 8.235979e-01
#> 408 DRB1*08:03 7.739671e-01
#> 409 DRB1*08:04 8.863330e-01
#> 410 DRB1*08:06 9.747476e-01
#> 411 DRB1*08:11 9.873786e-01
#> 412 DRB1*08:18 9.873786e-01
#> 413 DRB1*08:40 9.873786e-01
#> 414 DRB1*08:77 9.115621e-01
#> 415 DRB1*09:01 5.475507e-14
#> 416 DRB1*10:01 7.250487e-01
#> 417 DRB1*11:01 5.169113e-01
#> 418 DRB1*11:02 8.989411e-01
#> 419 DRB1*11:03 8.486181e-01
#> 420 DRB1*11:04 1.899495e-01
#> 421 DRB1*11:14 9.873786e-01
#> 422 DRB1*12:01 5.402271e-01
#> 423 DRB1*12:02 1.120573e-03
#> 424 DRB1*12:10 9.747476e-01
#> 425 DRB1*13:01 1.537580e-01
#> 426 DRB1*13:02 9.882807e-01
#> 427 DRB1*13:03 6.770363e-01
#> 428 DRB1*13:05 9.494700e-01
#> 429 DRB1*13:12 9.747476e-01
#> 430 DRB1*13:27 9.873786e-01
#> 431 DRB1*14:01 9.115621e-01
#> 432 DRB1*14:02 9.621104e-01
#> 433 DRB1*14:03 9.747476e-01
#> 434 DRB1*14:04 9.621104e-01
#> 435 DRB1*14:05 9.747476e-01
#> 436 DRB1*14:06 9.241927e-01
#> 437 DRB1*14:07 9.873786e-01
#> 438 DRB1*14:18 9.873786e-01
#> 439 DRB1*14:54 5.186921e-01
#> 440 DRB1*15:01 4.817173e-03
#> 441 DRB1*15:02 5.511430e-01
#> 442 DRB1*15:03 4.292086e-56
#> 443 DRB1*16:01 7.385183e-03
#> 444 DRB1*16:02 9.368297e-01
#> 445 DRB1*16:15 8.737410e-01
#> 446 DRB1*16:32 9.873786e-01
#> 447 DRB1*16:42 9.873786e-01
# get HWE in groups defined by disease status
# grouping by `disease == 1` will divide samples into two groups:
# `disease == 1` and `not disease == 1`
HWETest(midas, experiment = "hla_alleles", HWE_group = disease == 1)
#> var disease == 1 not disease == 1
#> 1 A*01:01 4.458834e-01 4.510815e-01
#> 2 A*01:02 9.642580e-01 NaN
#> 3 A*01:234 NaN 9.821424e-01
#> 4 A*01:237 NaN 9.821424e-01
#> 5 A*01:274 9.642580e-01 9.642580e-01
#> 6 A*01:43 9.821424e-01 NaN
#> 7 A*01:98 NaN 9.821424e-01
#> 8 A*02:01 8.667941e-01 8.010079e-01
#> 9 A*02:02 9.821424e-01 9.821424e-01
#> 10 A*02:03 9.463557e-01 9.284446e-01
#> 11 A*02:05 6.877874e-19 7.859394e-01
#> 12 A*02:06 1.418316e-03 1.501066e-06
#> 13 A*02:07 9.463557e-01 9.284446e-01
#> 14 A*02:08 NaN 9.642580e-01
#> 15 A*02:10 9.821424e-01 9.642580e-01
#> 16 A*02:211 9.821424e-01 NaN
#> 17 A*02:22 NaN 9.821424e-01
#> 18 A*02:324 NaN 9.821424e-01
#> 19 A*02:60 NaN 9.821424e-01
#> 20 A*02:614 NaN 9.821424e-01
#> 21 A*02:642 NaN 9.821424e-01
#> 22 A*02:686 NaN 9.821424e-01
#> 23 A*02:753 9.821424e-01 NaN
#> 24 A*02:763 NaN 9.821424e-01
#> 25 A*03:01 7.345401e-01 5.095385e-01
#> 26 A*03:02 8.926325e-01 8.747498e-01
#> 27 A*03:205 NaN 9.821424e-01
#> 28 A*03:24 9.821424e-01 NaN
#> 29 A*03:312 9.821424e-01 9.642580e-01
#> 30 A*03:72 9.821424e-01 9.821424e-01
#> 31 A*11:01 8.474123e-01 3.360577e-02
#> 32 A*11:02 NaN 9.821424e-01
#> 33 A*11:03 NaN 9.821424e-01
#> 34 A*11:12 NaN 9.821424e-01
#> 35 A*11:306 9.642580e-01 9.821424e-01
#> 36 A*11:43 NaN 9.821424e-01
#> 37 A*11:50Q NaN 9.821424e-01
#> 38 A*11:88 9.642580e-01 9.821424e-01
#> 39 A*23:01 6.314785e-01 5.505762e-01
#> 40 A*23:17 NaN 9.821424e-01
#> 41 A*23:18 9.821424e-01 NaN
#> 42 A*24:02 2.687114e-01 5.060263e-01
#> 43 A*24:03 9.821424e-01 9.821424e-01
#> 44 A*24:04 NaN 9.821424e-01
#> 45 A*24:07 9.505398e-111 NaN
#> 46 A*24:104 9.821424e-01 9.821424e-01
#> 47 A*24:20 9.642580e-01 9.642580e-01
#> 48 A*24:50 9.463557e-01 9.821424e-01
#> 49 A*24:95 9.821424e-01 NaN
#> 50 A*25:01 6.149636e-01 4.892090e-01
#> 51 A*25:09 NaN 9.642580e-01
#> 52 A*25:25 NaN 9.821424e-01
#> 53 A*26:01 3.034080e-01 3.370681e-01
#> 54 A*26:02 9.821424e-01 9.463557e-01
#> 55 A*26:03 9.821424e-01 9.821424e-01
#> 56 A*26:08 9.821424e-01 9.642580e-01
#> 57 A*26:16 9.821424e-01 NaN
#> 58 A*29:01 9.821424e-01 9.105338e-01
#> 59 A*29:02 6.481452e-01 2.071750e-01
#> 60 A*29:119 9.821424e-01 9.642580e-01
#> 61 A*30:01 6.989742e-01 6.481452e-01
#> 62 A*30:02 1.151375e-01 6.149636e-01
#> 63 A*30:04 9.821424e-01 9.642580e-01
#> 64 A*31:01 4.036917e-01 6.149636e-01
#> 65 A*31:08 9.821424e-01 NaN
#> 66 A*31:21 NaN 9.821424e-01
#> 67 A*32:01 5.505762e-01 4.597880e-01
#> 68 A*32:02 NaN 9.821424e-01
#> 69 A*32:116 9.463557e-01 9.821424e-01
#> 70 A*33:01 7.508685e-01 8.926325e-01
#> 71 A*33:03 8.747498e-01 8.390774e-01
#> 72 A*33:05 NaN 9.642580e-01
#> 73 A*33:125 NaN 9.821424e-01
#> 74 A*33:163 NaN 9.821424e-01
#> 75 A*33:51 NaN 9.821424e-01
#> 76 A*34:01 9.821424e-01 NaN
#> 77 A*34:02 9.105338e-01 9.821424e-01
#> 78 A*66:01 9.105338e-01 9.105338e-01
#> 79 A*68:01 2.071750e-01 5.194880e-01
#> 80 A*68:02 7.859394e-01 8.390774e-01
#> 81 A*68:04 NaN 9.821424e-01
#> 82 A*68:16 9.821424e-01 NaN
#> 83 A*68:164 NaN 9.821424e-01
#> 84 A*68:17 9.821424e-01 NaN
#> 85 A*68:23 9.821424e-01 NaN
#> 86 A*68:66 9.821424e-01 NaN
#> 87 A*69:01 9.463557e-01 9.463557e-01
#> 88 A*74:01 NaN 9.642580e-01
#> 89 B*07:02 2.143342e-02 9.714144e-01
#> 90 B*07:04 9.821424e-01 NaN
#> 91 B*07:05 9.821424e-01 9.284446e-01
#> 92 B*07:06 9.642580e-01 9.463557e-01
#> 93 B*07:10 9.821424e-01 NaN
#> 94 B*07:14 NaN 9.821424e-01
#> 95 B*07:22 9.821424e-01 NaN
#> 96 B*07:47 9.821424e-01 NaN
#> 97 B*08:01 7.185338e-01 1.585004e-01
#> 98 B*08:156 9.821424e-01 9.821424e-01
#> 99 B*08:94 NaN 9.821424e-01
#> 100 B*13:01 9.642580e-01 9.463557e-01
#> 101 B*13:02 2.438194e-03 7.337845e-01
#> 102 B*13:117 NaN 9.821424e-01
#> 103 B*14:01 7.859394e-01 8.213061e-01
#> 104 B*14:02 5.824204e-01 7.161655e-01
#> 105 B*14:28 NaN 9.821424e-01
#> 106 B*15:01 1.404105e-02 3.861508e-02
#> 107 B*15:02 9.821424e-01 9.105338e-01
#> 108 B*15:03 9.463557e-01 9.105338e-01
#> 109 B*15:07 9.642580e-01 NaN
#> 110 B*15:09 9.642580e-01 NaN
#> 111 B*15:10 9.284446e-01 NaN
#> 112 B*15:11 9.821424e-01 9.642580e-01
#> 113 B*15:12 9.821424e-01 NaN
#> 114 B*15:15 9.821424e-01 NaN
#> 115 B*15:17 9.105338e-01 9.105338e-01
#> 116 B*15:18 NaN 9.463557e-01
#> 117 B*15:20 9.821424e-01 NaN
#> 118 B*15:212 NaN 9.821424e-01
#> 119 B*15:220 9.821424e-01 NaN
#> 120 B*15:25 9.642580e-01 9.821424e-01
#> 121 B*15:256 9.821424e-01 NaN
#> 122 B*15:27 NaN 9.821424e-01
#> 123 B*15:39 NaN 9.821424e-01
#> 124 B*15:63 NaN 9.821424e-01
#> 125 B*18:01 3.041245e-01 3.922438e-01
#> 126 B*18:02 9.821424e-01 NaN
#> 127 B*18:03 NaN 9.821424e-01
#> 128 B*18:07 NaN 9.821424e-01
#> 129 B*27:02 9.284446e-01 9.105338e-01
#> 130 B*27:03 9.821424e-01 9.642580e-01
#> 131 B*27:04 9.821424e-01 9.821424e-01
#> 132 B*27:05 3.335070e-03 5.232419e-01
#> 133 B*27:06 9.821424e-01 NaN
#> 134 B*27:127 9.642580e-01 NaN
#> 135 B*27:14 9.821424e-01 NaN
#> 136 B*35:01 4.454132e-01 1.261788e-02
#> 137 B*35:02 9.463557e-01 1.124194e-04
#> 138 B*35:03 7.508685e-01 5.664072e-01
#> 139 B*35:05 9.505398e-111 NaN
#> 140 B*35:08 9.284446e-01 8.035904e-01
#> 141 B*35:09 9.821424e-01 NaN
#> 142 B*35:17 NaN 9.821424e-01
#> 143 B*35:194 9.821424e-01 NaN
#> 144 B*35:41 9.821424e-01 NaN
#> 145 B*35:42 9.821424e-01 NaN
#> 146 B*35:43 9.821424e-01 NaN
#> 147 B*35:60 NaN 9.821424e-01
#> 148 B*35:67 9.821424e-01 NaN
#> 149 B*35:71 NaN 9.821424e-01
#> 150 B*37:01 7.683624e-01 7.859394e-01
#> 151 B*37:68 NaN 9.821424e-01
#> 152 B*38:01 2.071750e-01 3.177626e-01
#> 153 B*38:02 9.463557e-01 9.642580e-01
#> 154 B*39:01 8.035904e-01 6.819014e-01
#> 155 B*39:05 9.821424e-01 NaN
#> 156 B*39:06 9.284446e-01 8.926325e-01
#> 157 B*39:09 9.821424e-01 NaN
#> 158 B*40:01 4.743884e-01 2.793337e-01
#> 159 B*40:02 8.390774e-01 6.649556e-01
#> 160 B*40:06 1.501066e-06 8.568950e-01
#> 161 B*40:117 9.821424e-01 NaN
#> 162 B*40:21 NaN 9.821424e-01
#> 163 B*40:32 9.821424e-01 NaN
#> 164 B*40:353 9.821424e-01 NaN
#> 165 B*40:49 9.821424e-01 NaN
#> 166 B*41:01 9.642580e-01 8.747498e-01
#> 167 B*41:02 9.105338e-01 9.284446e-01
#> 168 B*42:01 9.284446e-01 9.821424e-01
#> 169 B*42:02 9.642580e-01 NaN
#> 170 B*44:02 3.494980e-01 3.545424e-01
#> 171 B*44:03 2.140040e-01 2.920457e-01
#> 172 B*44:04 NaN 9.821424e-01
#> 173 B*44:05 9.463557e-01 9.642580e-01
#> 174 B*44:06 9.821424e-01 NaN
#> 175 B*44:27 9.463557e-01 8.747498e-01
#> 176 B*44:270 9.642580e-01 NaN
#> 177 B*44:37 NaN 9.821424e-01
#> 178 B*44:55 9.821424e-01 NaN
#> 179 B*45:01 8.747498e-01 8.568950e-01
#> 180 B*46:01 9.284446e-01 8.747498e-01
#> 181 B*47:01 9.105338e-01 9.821424e-01
#> 182 B*47:04 9.642580e-01 NaN
#> 183 B*48:01 8.568950e-01 4.143911e-50
#> 184 B*49:01 6.314785e-01 1.151375e-01
#> 185 B*50:01 7.334665e-01 7.161655e-01
#> 186 B*50:02 NaN 9.821424e-01
#> 187 B*51:01 4.417170e-01 5.180541e-01
#> 188 B*51:02 9.821424e-01 NaN
#> 189 B*51:05 9.821424e-01 NaN
#> 190 B*51:07 NaN 9.284446e-01
#> 191 B*51:08 9.821424e-01 9.105338e-01
#> 192 B*51:09 9.821424e-01 NaN
#> 193 B*51:173Q 9.821424e-01 NaN
#> 194 B*51:203 NaN 9.821424e-01
#> 195 B*51:230 9.821424e-01 NaN
#> 196 B*52:01 6.314785e-01 1.151375e-01
#> 197 B*53:01 9.284446e-01 9.284446e-01
#> 198 B*54:01 8.747498e-01 9.105338e-01
#> 199 B*55:01 7.683624e-01 4.926837e-02
#> 200 B*55:02 9.105338e-01 9.463557e-01
#> 201 B*56:01 8.568950e-01 8.390774e-01
#> 202 B*56:03 9.821424e-01 NaN
#> 203 B*56:09 NaN 9.821424e-01
#> 204 B*57:01 5.508523e-01 1.151375e-01
#> 205 B*57:02 8.926325e-01 9.821424e-01
#> 206 B*57:03 8.926325e-01 NaN
#> 207 B*58:01 8.747498e-01 7.334665e-01
#> 208 B*58:02 9.463557e-01 9.642580e-01
#> 209 B*59:01 NaN 9.642580e-01
#> 210 B*67:01 9.821424e-01 NaN
#> 211 B*73:01 NaN 9.642580e-01
#> 212 C*01:02 5.566223e-01 2.595610e-01
#> 213 C*01:03 NaN 9.642580e-01
#> 214 C*01:103 NaN 9.821424e-01
#> 215 C*01:22 NaN 9.821424e-01
#> 216 C*01:51 9.821424e-01 NaN
#> 217 C*02:02 9.896214e-01 9.346065e-01
#> 218 C*02:06 NaN 9.821424e-01
#> 219 C*02:10 9.463557e-01 9.105338e-01
#> 220 C*02:20 NaN 9.821424e-01
#> 221 C*03:02 9.284446e-01 8.390774e-01
#> 222 C*03:03 5.655567e-01 4.065879e-01
#> 223 C*03:04 9.528671e-01 1.939416e-04
#> 224 C*03:05 NaN 9.821424e-01
#> 225 C*03:06 9.821424e-01 NaN
#> 226 C*03:344 9.463557e-01 9.821424e-01
#> 227 C*03:39 9.821424e-01 9.642580e-01
#> 228 C*03:85 NaN 9.821424e-01
#> 229 C*04:01 7.750978e-01 1.382501e-02
#> 230 C*04:03 9.821424e-01 9.642580e-01
#> 231 C*04:277 NaN 9.821424e-01
#> 232 C*05:01 5.146674e-01 1.170605e-01
#> 233 C*05:05 9.821424e-01 NaN
#> 234 C*05:37 9.821424e-01 NaN
#> 235 C*06:02 2.661323e-01 8.800755e-01
#> 236 C*06:09 NaN 9.821424e-01
#> 237 C*07:01 6.643130e-01 6.540518e-01
#> 238 C*07:02 7.747196e-01 3.607264e-01
#> 239 C*07:04 7.508685e-01 6.481452e-01
#> 240 C*07:18 9.463557e-01 8.747498e-01
#> 241 C*07:204 9.821424e-01 NaN
#> 242 C*07:51 9.642580e-01 NaN
#> 243 C*07:578 9.284446e-01 9.463557e-01
#> 244 C*07:615 NaN 9.821424e-01
#> 245 C*07:696 9.821424e-01 9.821424e-01
#> 246 C*08:01 8.213061e-01 7.859394e-01
#> 247 C*08:02 2.920457e-01 2.793337e-01
#> 248 C*08:03 8.926325e-01 4.143911e-50
#> 249 C*12:02 6.481452e-01 1.432546e-01
#> 250 C*12:03 5.785555e-02 4.101504e-01
#> 251 C*12:132 9.821424e-01 NaN
#> 252 C*12:167 NaN 9.821424e-01
#> 253 C*12:28 9.821424e-01 NaN
#> 254 C*14:02 7.508685e-01 7.334665e-01
#> 255 C*14:03 9.463557e-01 9.642580e-01
#> 256 C*15:02 5.986083e-01 5.824204e-01
#> 257 C*15:05 9.284446e-01 8.568950e-01
#> 258 C*15:07 9.821424e-01 NaN
#> 259 C*15:09 9.821424e-01 NaN
#> 260 C*16:01 5.824204e-01 5.664072e-01
#> 261 C*16:02 9.284446e-01 7.859394e-01
#> 262 C*16:04 9.821424e-01 9.463557e-01
#> 263 C*17:01 9.105338e-01 8.926325e-01
#> 264 C*17:03 8.926325e-01 9.284446e-01
#> 265 C*18:02 9.463557e-01 NaN
#> 266 DPA1*01:03 3.031189e-01 2.951598e-04
#> 267 DPA1*01:04 8.390774e-01 9.463557e-01
#> 268 DPA1*01:05 NaN 9.821424e-01
#> 269 DPA1*01:11 NaN 9.821424e-01
#> 270 DPA1*02:01 5.853393e-01 2.771441e-02
#> 271 DPA1*02:02 1.435600e-13 9.804817e-13
#> 272 DPA1*02:06 9.284446e-01 9.105338e-01
#> 273 DPA1*02:07 8.568950e-01 9.105338e-01
#> 274 DPA1*03:01 9.284446e-01 9.284446e-01
#> 275 DPA1*04:01 9.821424e-01 NaN
#> 276 DPB1*01:01 6.501129e-01 7.337845e-01
#> 277 DPB1*02:01 8.533282e-01 3.342930e-02
#> 278 DPB1*02:02 8.035904e-01 4.926837e-02
#> 279 DPB1*03:01 5.888546e-01 7.572197e-01
#> 280 DPB1*04:01 2.970852e-02 4.586521e-04
#> 281 DPB1*04:02 3.743689e-01 1.588829e-01
#> 282 DPB1*05:01 3.024316e-17 8.416915e-02
#> 283 DPB1*06:01 8.568950e-01 1.124194e-04
#> 284 DPB1*09:01 8.035904e-01 8.390774e-01
#> 285 DPB1*104:01 6.819014e-01 1.721583e-02
#> 286 DPB1*105:01 8.568950e-01 8.926325e-01
#> 287 DPB1*107:01 9.821424e-01 NaN
#> 288 DPB1*10:01 8.035904e-01 7.508685e-01
#> 289 DPB1*113:01 NaN 9.642580e-01
#> 290 DPB1*11:01 6.481452e-01 6.481452e-01
#> 291 DPB1*124:01 8.747498e-01 9.105338e-01
#> 292 DPB1*126:01 9.105338e-01 9.642580e-01
#> 293 DPB1*131:01 9.821424e-01 9.821424e-01
#> 294 DPB1*133:01 NaN 9.821424e-01
#> 295 DPB1*135:01 9.642580e-01 9.284446e-01
#> 296 DPB1*138:01 9.821424e-01 NaN
#> 297 DPB1*13:01 6.314785e-01 1.721583e-02
#> 298 DPB1*14:01 8.995742e-02 6.819014e-01
#> 299 DPB1*150:01 9.821424e-01 NaN
#> 300 DPB1*158:01 9.821424e-01 NaN
#> 301 DPB1*15:01 8.390774e-01 9.284446e-01
#> 302 DPB1*162:01 9.463557e-01 9.642580e-01
#> 303 DPB1*16:01 9.284446e-01 8.926325e-01
#> 304 DPB1*17:01 8.995742e-02 3.177626e-01
#> 305 DPB1*18:01 9.821424e-01 NaN
#> 306 DPB1*19:01 9.284446e-01 9.463557e-01
#> 307 DPB1*20:01 9.284446e-01 9.463557e-01
#> 308 DPB1*21:01 9.821424e-01 9.463557e-01
#> 309 DPB1*22:01 NaN 9.821424e-01
#> 310 DPB1*234:01 NaN 9.821424e-01
#> 311 DPB1*23:01 8.390774e-01 8.926325e-01
#> 312 DPB1*259:01 9.821424e-01 NaN
#> 313 DPB1*271:01 9.642580e-01 9.642580e-01
#> 314 DPB1*294:01 9.821424e-01 NaN
#> 315 DPB1*33:01 9.821424e-01 NaN
#> 316 DPB1*350:01 8.926325e-01 9.821424e-01
#> 317 DPB1*351:01 9.821424e-01 9.642580e-01
#> 318 DPB1*36:01 NaN 9.821424e-01
#> 319 DPB1*38:01 NaN 9.821424e-01
#> 320 DPB1*398:01 9.821424e-01 NaN
#> 321 DPB1*40:01 9.821424e-01 NaN
#> 322 DPB1*414:01 9.284446e-01 9.463557e-01
#> 323 DPB1*41:01 NaN 9.821424e-01
#> 324 DPB1*45:01 9.821424e-01 NaN
#> 325 DPB1*461:01 9.821424e-01 NaN
#> 326 DPB1*462:01 NaN 9.821424e-01
#> 327 DPB1*463:01 9.821424e-01 9.463557e-01
#> 328 DPB1*47:01 9.821424e-01 NaN
#> 329 DPB1*519:01 9.821424e-01 NaN
#> 330 DPB1*51:01 9.821424e-01 NaN
#> 331 DPB1*547:01 9.821424e-01 NaN
#> 332 DPB1*57:01 9.821424e-01 9.642580e-01
#> 333 DPB1*651:01 9.284446e-01 NaN
#> 334 DPB1*702:01 9.284446e-01 9.463557e-01
#> 335 DPB1*744:01 9.821424e-01 NaN
#> 336 DPB1*80:01 9.821424e-01 NaN
#> 337 DPB1*88:01 NaN 9.821424e-01
#> 338 DPB1*92:01 9.821424e-01 NaN
#> 339 DQA1*01:01 7.763217e-01 8.132882e-02
#> 340 DQA1*01:02 1.561554e-01 2.362403e-01
#> 341 DQA1*01:03 4.910020e-01 9.273485e-02
#> 342 DQA1*01:04 5.986083e-01 5.042442e-01
#> 343 DQA1*01:05 8.035904e-01 7.508685e-01
#> 344 DQA1*01:06 9.821424e-01 NaN
#> 345 DQA1*01:10 9.821424e-01 9.821424e-01
#> 346 DQA1*02:01 1.403811e-02 6.348000e-01
#> 347 DQA1*03:01 6.270325e-01 6.004429e-01
#> 348 DQA1*03:02 3.398993e-02 1.418316e-03
#> 349 DQA1*03:03 8.972508e-01 3.927654e-01
#> 350 DQA1*04:01 7.337845e-01 6.481452e-01
#> 351 DQA1*04:02 NaN 9.642580e-01
#> 352 DQA1*05:01 5.814609e-01 2.051846e-03
#> 353 DQA1*05:03 8.926325e-01 7.508685e-01
#> 354 DQA1*05:05 6.956462e-01 4.051686e-01
#> 355 DQA1*05:06 NaN 9.821424e-01
#> 356 DQA1*05:07 9.821424e-01 NaN
#> 357 DQA1*05:08 9.821424e-01 NaN
#> 358 DQA1*05:09 9.463557e-01 9.463557e-01
#> 359 DQA1*06:01 1.124194e-04 8.035904e-01
#> 360 DQB1*02:01 4.390796e-01 2.051846e-03
#> 361 DQB1*02:02 3.260894e-05 4.786006e-01
#> 362 DQB1*02:10 9.821424e-01 NaN
#> 363 DQB1*03:01 5.645883e-02 2.530537e-01
#> 364 DQB1*03:02 6.270325e-01 4.417170e-01
#> 365 DQB1*03:03 3.041245e-01 4.454132e-01
#> 366 DQB1*03:04 9.105338e-01 9.642580e-01
#> 367 DQB1*03:05 9.463557e-01 NaN
#> 368 DQB1*03:19 8.747498e-01 9.284446e-01
#> 369 DQB1*03:22 8.213061e-01 7.859394e-01
#> 370 DQB1*03:251 9.642580e-01 NaN
#> 371 DQB1*03:96 9.821424e-01 9.284446e-01
#> 372 DQB1*04:01 2.450294e-11 7.683624e-01
#> 373 DQB1*04:02 4.173604e-01 5.986083e-01
#> 374 DQB1*04:23 9.642580e-01 9.821424e-01
#> 375 DQB1*05:01 4.448428e-01 3.800165e-01
#> 376 DQB1*05:02 3.335070e-03 8.956533e-01
#> 377 DQB1*05:03 6.314785e-01 5.349342e-01
#> 378 DQB1*05:04 9.821424e-01 9.463557e-01
#> 379 DQB1*05:107 9.821424e-01 NaN
#> 380 DQB1*06:01 5.505762e-01 5.524207e-04
#> 381 DQB1*06:02 8.444182e-01 1.531837e-03
#> 382 DQB1*06:03 7.547216e-01 2.257310e-01
#> 383 DQB1*06:04 4.036917e-01 5.655567e-01
#> 384 DQB1*06:07 9.821424e-01 NaN
#> 385 DQB1*06:09 8.390774e-01 8.390774e-01
#> 386 DRA*01:01 2.789248e-01 3.601145e-01
#> 387 DRA*01:02 2.789248e-01 3.601145e-01
#> 388 DRB1*01:01 8.739948e-01 1.473929e-02
#> 389 DRB1*01:02 1.151375e-01 1.325122e-02
#> 390 DRB1*01:03 8.568950e-01 9.821424e-01
#> 391 DRB1*03:01 3.743689e-01 1.602258e-03
#> 392 DRB1*03:02 9.284446e-01 NaN
#> 393 DRB1*03:07 NaN 9.821424e-01
#> 394 DRB1*04:01 6.884533e-01 5.841735e-02
#> 395 DRB1*04:02 1.501066e-06 8.035904e-01
#> 396 DRB1*04:03 1.151375e-01 7.508685e-01
#> 397 DRB1*04:04 6.149636e-01 2.423752e-01
#> 398 DRB1*04:05 3.335070e-03 5.986083e-01
#> 399 DRB1*04:06 9.642580e-01 8.926325e-01
#> 400 DRB1*04:07 8.213061e-01 1.790460e-13
#> 401 DRB1*04:08 9.642580e-01 9.105338e-01
#> 402 DRB1*04:10 9.642580e-01 NaN
#> 403 DRB1*04:13 9.821424e-01 NaN
#> 404 DRB1*04:92 9.821424e-01 NaN
#> 405 DRB1*07:01 3.160062e-03 6.348000e-01
#> 406 DRB1*08:01 4.926837e-02 7.683624e-01
#> 407 DRB1*08:02 8.213061e-01 9.284446e-01
#> 408 DRB1*08:03 8.390774e-01 8.390774e-01
#> 409 DRB1*08:04 8.747498e-01 9.642580e-01
#> 410 DRB1*08:06 9.821424e-01 9.821424e-01
#> 411 DRB1*08:11 NaN 9.821424e-01
#> 412 DRB1*08:18 NaN 9.821424e-01
#> 413 DRB1*08:40 NaN 9.821424e-01
#> 414 DRB1*08:77 9.284446e-01 9.463557e-01
#> 415 DRB1*09:01 1.672301e-10 4.644607e-04
#> 416 DRB1*10:01 8.390774e-01 7.683624e-01
#> 417 DRB1*11:01 7.147688e-01 6.655523e-01
#> 418 DRB1*11:02 9.284446e-01 9.284446e-01
#> 419 DRB1*11:03 8.926325e-01 8.926325e-01
#> 420 DRB1*11:04 2.725558e-01 4.429119e-01
#> 421 DRB1*11:14 9.821424e-01 NaN
#> 422 DRB1*12:01 6.819014e-01 6.481452e-01
#> 423 DRB1*12:02 1.124194e-04 8.747498e-01
#> 424 DRB1*12:10 NaN 9.642580e-01
#> 425 DRB1*13:01 6.748768e-01 9.942882e-02
#> 426 DRB1*13:02 2.809499e-01 2.424790e-01
#> 427 DRB1*13:03 7.508685e-01 7.859394e-01
#> 428 DRB1*13:05 9.642580e-01 9.642580e-01
#> 429 DRB1*13:12 NaN 9.642580e-01
#> 430 DRB1*13:27 NaN 9.821424e-01
#> 431 DRB1*14:01 9.284446e-01 9.463557e-01
#> 432 DRB1*14:02 9.642580e-01 9.821424e-01
#> 433 DRB1*14:03 9.821424e-01 9.821424e-01
#> 434 DRB1*14:04 9.463557e-01 NaN
#> 435 DRB1*14:05 9.642580e-01 NaN
#> 436 DRB1*14:06 9.642580e-01 9.284446e-01
#> 437 DRB1*14:07 NaN 9.821424e-01
#> 438 DRB1*14:18 NaN 9.821424e-01
#> 439 DRB1*14:54 7.334665e-01 5.664072e-01
#> 440 DRB1*15:01 3.695519e-01 1.097330e-03
#> 441 DRB1*15:02 6.819014e-01 6.649556e-01
#> 442 DRB1*15:03 9.642580e-01 9.505398e-111
#> 443 DRB1*16:01 3.475184e-03 2.071750e-01
#> 444 DRB1*16:02 9.642580e-01 9.463557e-01
#> 445 DRB1*16:15 9.821424e-01 8.390774e-01
#> 446 DRB1*16:32 9.821424e-01 NaN
#> 447 DRB1*16:42 9.821424e-01 NaN
# filter MiDAS object by HWE test p-value
HWETest(midas, experiment = "hla_alleles", HWE_cutoff = 0.05, as.MiDAS = TRUE)
#> A MiDAS object of 1 listed
#> experiment with a user-defined name and respective class.
#> Containing an ExperimentList class object of length 1:
#> [1] hla_alleles: SummarizedExperiment with 412 rows and 1000 columns
#> Functionality:
#> experiments() - obtain the ExperimentList instance
#> colData() - the primary/phenotype DataFrame
#> sampleMap() - the sample coordination DataFrame
#> `$`, `[`, `[[` - extract colData columns, subset, or experiment
#> *Format() - convert into a long or wide DataFrame
#> assays() - convert ExperimentList to a SimpleList of matrices
#> exportClass() - save data to flat files