Get sample/alteration blocks
Examples
# \donttest{
data(luad_run_data, package = "SelectSim")
al <- new.AL.general(luad_run_data$M,
feat.covariates = luad_run_data$alteration.class,
sample.covariates = luad_run_data$sample.class,
min.freq = 10)
get.blocks(al)
#> $sample.blocks
#> $sample.blocks$LUAD
#> TCGA-05-4244-01 TCGA-05-4249-01 TCGA-05-4250-01 TCGA-05-4382-01 TCGA-05-4384-01
#> 1 2 3 4 5
#> TCGA-05-4389-01 TCGA-05-4390-01 TCGA-05-4395-01 TCGA-05-4396-01 TCGA-05-4397-01
#> 6 7 8 9 10
#> TCGA-05-4403-01 TCGA-05-4405-01 TCGA-05-4410-01 TCGA-05-4415-01 TCGA-05-4417-01
#> 11 12 13 14 15
#> TCGA-05-4418-01 TCGA-05-4420-01 TCGA-05-4422-01 TCGA-05-4425-01 TCGA-05-4427-01
#> 16 17 18 19 20
#> TCGA-05-4430-01 TCGA-05-4432-01 TCGA-05-4433-01 TCGA-05-5423-01 TCGA-05-5425-01
#> 21 22 23 24 25
#> TCGA-05-5428-01 TCGA-05-5429-01 TCGA-35-3615-01 TCGA-35-4122-01 TCGA-35-4123-01
#> 26 27 28 29 30
#> TCGA-35-5375-01 TCGA-38-4625-01 TCGA-38-4627-01 TCGA-38-4631-01 TCGA-38-4632-01
#> 31 32 33 34 35
#> TCGA-38-6178-01 TCGA-44-2656-01 TCGA-44-2657-01 TCGA-44-2662-01 TCGA-44-2665-01
#> 36 37 38 39 40
#> TCGA-44-2666-01 TCGA-44-2668-01 TCGA-44-3396-01 TCGA-44-5643-01 TCGA-44-5645-01
#> 41 42 43 44 45
#> TCGA-44-6145-01 TCGA-44-6146-01 TCGA-44-6774-01 TCGA-44-6775-01 TCGA-44-6776-01
#> 46 47 48 49 50
#> TCGA-44-6777-01 TCGA-44-7659-01 TCGA-44-7661-01 TCGA-44-7662-01 TCGA-44-7670-01
#> 51 52 53 54 55
#> TCGA-44-7671-01 TCGA-44-7672-01 TCGA-44-8117-01 TCGA-44-8119-01 TCGA-44-8120-01
#> 56 57 58 59 60
#> TCGA-44-A47A-01 TCGA-44-A47G-01 TCGA-44-A4SS-01 TCGA-44-A4SU-01 TCGA-49-4486-01
#> 61 62 63 64 65
#> TCGA-49-4488-01 TCGA-49-4490-01 TCGA-49-4494-01 TCGA-49-4505-01 TCGA-49-4506-01
#> 66 67 68 69 70
#> TCGA-49-4507-01 TCGA-49-4510-01 TCGA-49-4514-01 TCGA-49-6744-01 TCGA-49-6745-01
#> 71 72 73 74 75
#> TCGA-49-AAQV-01 TCGA-49-AAR9-01 TCGA-49-AARE-01 TCGA-49-AARN-01 TCGA-49-AARO-01
#> 76 77 78 79 80
#> TCGA-49-AARQ-01 TCGA-4B-A93V-01 TCGA-50-5044-01 TCGA-50-5051-01 TCGA-50-5066-01
#> 81 82 83 84 85
#> TCGA-50-5068-01 TCGA-50-5930-01 TCGA-50-5932-01 TCGA-50-5933-01 TCGA-50-5936-01
#> 86 87 88 89 90
#> TCGA-50-5939-01 TCGA-50-5941-01 TCGA-50-5942-01 TCGA-50-5944-01 TCGA-50-5946-01
#> 91 92 93 94 95
#> TCGA-50-6591-01 TCGA-50-6592-01 TCGA-50-6593-01 TCGA-50-6594-01 TCGA-50-6595-01
#> 96 97 98 99 100
#> TCGA-50-6673-01 TCGA-50-7109-01 TCGA-50-8459-01 TCGA-50-8460-01 TCGA-53-7626-01
#> 101 102 103 104 105
#> TCGA-53-7813-01 TCGA-53-A4EZ-01 TCGA-55-1592-01 TCGA-55-1595-01 TCGA-55-1596-01
#> 106 107 108 109 110
#> TCGA-55-6642-01 TCGA-55-6968-01 TCGA-55-6969-01 TCGA-55-6970-01 TCGA-55-6975-01
#> 111 112 113 114 115
#> TCGA-55-6979-01 TCGA-55-6981-01 TCGA-55-6983-01 TCGA-55-6984-01 TCGA-55-7281-01
#> 116 117 118 119 120
#> TCGA-55-7283-01 TCGA-55-7284-01 TCGA-55-7570-01 TCGA-55-7573-01 TCGA-55-7576-01
#> 121 122 123 124 125
#> TCGA-55-7724-01 TCGA-55-7725-01 TCGA-55-7726-01 TCGA-55-7727-01 TCGA-55-7728-01
#> 126 127 128 129 130
#> TCGA-55-7815-01 TCGA-55-7903-01 TCGA-55-7907-01 TCGA-55-7910-01 TCGA-55-7911-01
#> 131 132 133 134 135
#> TCGA-55-7913-01 TCGA-55-7914-01 TCGA-55-7994-01 TCGA-55-7995-01 TCGA-55-8085-01
#> 136 137 138 139 140
#> TCGA-55-8089-01 TCGA-55-8090-01 TCGA-55-8092-01 TCGA-55-8094-01 TCGA-55-8096-01
#> 141 142 143 144 145
#> TCGA-55-8097-01 TCGA-55-8203-01 TCGA-55-8205-01 TCGA-55-8207-01 TCGA-55-8208-01
#> 146 147 148 149 150
#> TCGA-55-8299-01 TCGA-55-8301-01 TCGA-55-8302-01 TCGA-55-8505-01 TCGA-55-8506-01
#> 151 152 153 154 155
#> TCGA-55-8508-01 TCGA-55-8511-01 TCGA-55-8512-01 TCGA-55-8514-01 TCGA-55-8614-01
#> 156 157 158 159 160
#> TCGA-55-8615-01 TCGA-55-8616-01 TCGA-55-8620-01 TCGA-55-A48X-01 TCGA-55-A48Y-01
#> 161 162 163 164 165
#> TCGA-55-A48Z-01 TCGA-55-A490-01 TCGA-55-A491-01 TCGA-55-A492-01 TCGA-55-A493-01
#> 166 167 168 169 170
#> TCGA-55-A494-01 TCGA-55-A4DG-01 TCGA-55-A57B-01 TCGA-62-8394-01 TCGA-62-8395-01
#> 171 172 173 174 175
#> TCGA-62-8398-01 TCGA-62-8399-01 TCGA-62-8402-01 TCGA-62-A46R-01 TCGA-62-A46S-01
#> 176 177 178 179 180
#> TCGA-62-A46U-01 TCGA-62-A46V-01 TCGA-62-A470-01 TCGA-62-A471-01 TCGA-62-A472-01
#> 181 182 183 184 185
#> TCGA-64-1676-01 TCGA-64-1677-01 TCGA-64-1679-01 TCGA-64-1680-01 TCGA-64-1681-01
#> 186 187 188 189 190
#> TCGA-64-5774-01 TCGA-64-5775-01 TCGA-64-5778-01 TCGA-64-5815-01 TCGA-67-3771-01
#> 191 192 193 194 195
#> TCGA-67-3772-01 TCGA-67-3773-01 TCGA-67-3774-01 TCGA-67-4679-01 TCGA-67-6215-01
#> 196 197 198 199 200
#> TCGA-67-6216-01 TCGA-67-6217-01 TCGA-69-7765-01 TCGA-69-7973-01 TCGA-69-7974-01
#> 201 202 203 204 205
#> TCGA-69-7978-01 TCGA-69-7980-01 TCGA-69-8253-01 TCGA-69-8254-01 TCGA-73-4658-01
#> 206 207 208 209 210
#> TCGA-73-4662-01 TCGA-73-4666-01 TCGA-73-4670-01 TCGA-73-4676-01 TCGA-73-4677-01
#> 211 212 213 214 215
#> TCGA-73-7498-01 TCGA-73-7499-01 TCGA-73-A9RS-01 TCGA-75-5126-01 TCGA-75-5146-01
#> 216 217 218 219 220
#> TCGA-75-5147-01 TCGA-75-6206-01 TCGA-75-6211-01 TCGA-75-6214-01 TCGA-75-7027-01
#> 221 222 223 224 225
#> TCGA-75-7030-01 TCGA-78-7145-01 TCGA-78-7146-01 TCGA-78-7147-01 TCGA-78-7148-01
#> 226 227 228 229 230
#> TCGA-78-7149-01 TCGA-78-7150-01 TCGA-78-7152-01 TCGA-78-7153-01 TCGA-78-7155-01
#> 231 232 233 234 235
#> TCGA-78-7158-01 TCGA-78-7159-01 TCGA-78-7160-01 TCGA-78-7161-01 TCGA-78-7166-01
#> 236 237 238 239 240
#> TCGA-78-7167-01 TCGA-78-7220-01 TCGA-78-7537-01 TCGA-78-7539-01 TCGA-78-7540-01
#> 241 242 243 244 245
#> TCGA-78-7633-01 TCGA-78-8640-01 TCGA-78-8655-01 TCGA-78-8660-01 TCGA-78-8662-01
#> 246 247 248 249 250
#> TCGA-80-5607-01 TCGA-80-5608-01 TCGA-83-5908-01 TCGA-86-6851-01 TCGA-86-7711-01
#> 251 252 253 254 255
#> TCGA-86-7713-01 TCGA-86-7714-01 TCGA-86-7953-01 TCGA-86-7954-01 TCGA-86-8054-01
#> 256 257 258 259 260
#> TCGA-86-8055-01 TCGA-86-8056-01 TCGA-86-8074-01 TCGA-86-8075-01 TCGA-86-8076-01
#> 261 262 263 264 265
#> TCGA-86-8278-01 TCGA-86-8279-01 TCGA-86-8280-01 TCGA-86-8281-01 TCGA-86-8359-01
#> 266 267 268 269 270
#> TCGA-86-8585-01 TCGA-86-8668-01 TCGA-86-8673-01 TCGA-86-8674-01 TCGA-86-A456-01
#> 271 272 273 274 275
#> TCGA-86-A4JF-01 TCGA-86-A4P7-01 TCGA-91-6828-01 TCGA-91-6829-01 TCGA-91-6830-01
#> 276 277 278 279 280
#> TCGA-91-6835-01 TCGA-91-6836-01 TCGA-91-6840-01 TCGA-91-6847-01 TCGA-91-6848-01
#> 281 282 283 284 285
#> TCGA-91-6849-01 TCGA-91-A4BD-01 TCGA-93-7347-01 TCGA-93-7348-01 TCGA-93-8067-01
#> 286 287 288 289 290
#> TCGA-93-A4JN-01 TCGA-93-A4JO-01 TCGA-93-A4JP-01 TCGA-95-7039-01 TCGA-95-7043-01
#> 291 292 293 294 295
#> TCGA-95-7562-01 TCGA-95-7567-01 TCGA-95-7944-01 TCGA-95-7947-01 TCGA-95-7948-01
#> 296 297 298 299 300
#> TCGA-95-A4VK-01 TCGA-95-A4VN-01 TCGA-95-A4VP-01 TCGA-97-7546-01 TCGA-97-7553-01
#> 301 302 303 304 305
#> TCGA-97-7554-01 TCGA-97-7937-01 TCGA-97-7938-01 TCGA-97-7941-01 TCGA-97-8171-01
#> 306 307 308 309 310
#> TCGA-97-8174-01 TCGA-97-8175-01 TCGA-97-8176-01 TCGA-97-8177-01 TCGA-97-8179-01
#> 311 312 313 314 315
#> TCGA-97-8547-01 TCGA-97-A4LX-01 TCGA-97-A4M0-01 TCGA-97-A4M1-01 TCGA-97-A4M3-01
#> 316 317 318 319 320
#> TCGA-97-A4M5-01 TCGA-97-A4M7-01 TCGA-99-8025-01 TCGA-99-8028-01 TCGA-99-8032-01
#> 321 322 323 324 325
#> TCGA-99-8033-01 TCGA-J2-8194-01 TCGA-J2-A4AD-01 TCGA-J2-A4AG-01 TCGA-L4-A4E5-01
#> 326 327 328 329 330
#> TCGA-L9-A443-01 TCGA-L9-A444-01 TCGA-L9-A50W-01 TCGA-L9-A5IP-01 TCGA-L9-A743-01
#> 331 332 333 334 335
#> TCGA-L9-A7SV-01 TCGA-L9-A8F4-01 TCGA-MN-A4N1-01 TCGA-MN-A4N4-01 TCGA-MN-A4N5-01
#> 336 337 338 339 340
#> TCGA-MP-A4SV-01 TCGA-MP-A4SW-01 TCGA-MP-A4SY-01 TCGA-MP-A4T4-01 TCGA-MP-A4T7-01
#> 341 342 343 344 345
#> TCGA-MP-A4T8-01 TCGA-MP-A4T9-01 TCGA-MP-A4TA-01 TCGA-MP-A4TD-01 TCGA-MP-A4TE-01
#> 346 347 348 349 350
#> TCGA-MP-A4TF-01 TCGA-MP-A4TI-01 TCGA-MP-A4TK-01 TCGA-NJ-A4YG-01 TCGA-NJ-A4YI-01
#> 351 352 353 354 355
#> TCGA-NJ-A4YP-01 TCGA-NJ-A4YQ-01 TCGA-NJ-A55O-01 TCGA-NJ-A55R-01 TCGA-05-4398-01
#> 356 357 358 359 360
#> TCGA-05-4402-01 TCGA-05-4424-01 TCGA-05-4426-01 TCGA-05-4434-01 TCGA-05-5715-01
#> 361 362 363 364 365
#> TCGA-38-4626-01 TCGA-38-4628-01 TCGA-38-7271-01 TCGA-38-A44F-01 TCGA-44-2655-01
#> 366 367 368 369 370
#> TCGA-44-2659-01 TCGA-44-3398-01 TCGA-44-3918-01 TCGA-44-3919-01 TCGA-44-4112-01
#> 371 372 373 374 375
#> TCGA-44-5644-01 TCGA-44-6148-01 TCGA-44-6778-01 TCGA-44-6779-01 TCGA-44-7660-01
#> 376 377 378 379 380
#> TCGA-44-7667-01 TCGA-44-7669-01 TCGA-44-A479-01 TCGA-44-A47B-01 TCGA-49-4487-01
#> 381 382 383 384 385
#> TCGA-49-4501-01 TCGA-49-4512-01 TCGA-49-6742-01 TCGA-49-6743-01 TCGA-49-6761-01
#> 386 387 388 389 390
#> TCGA-49-6767-01 TCGA-49-AAR0-01 TCGA-49-AAR2-01 TCGA-49-AAR3-01 TCGA-49-AAR4-01
#> 391 392 393 394 395
#> TCGA-49-AARR-01 TCGA-50-5045-01 TCGA-50-5049-01 TCGA-50-5055-01 TCGA-50-5072-01
#> 396 397 398 399 400
#> TCGA-50-5931-01 TCGA-50-5935-01 TCGA-50-6590-01 TCGA-50-6597-01 TCGA-50-8457-01
#> 401 402 403 404 405
#> TCGA-53-7624-01 TCGA-55-1594-01 TCGA-55-5899-01 TCGA-55-6543-01 TCGA-55-6712-01
#> 406 407 408 409 410
#> TCGA-55-6971-01 TCGA-55-6972-01 TCGA-55-6978-01 TCGA-55-6980-01 TCGA-55-6982-01
#> 411 412 413 414 415
#> TCGA-55-6985-01 TCGA-55-6986-01 TCGA-55-6987-01 TCGA-55-7574-01 TCGA-55-8087-01
#> 416 417 418 419 420
#> TCGA-55-8091-01 TCGA-55-8204-01 TCGA-55-8206-01 TCGA-55-8507-01 TCGA-55-8510-01
#> 421 422 423 424 425
#> TCGA-55-8513-01 TCGA-55-8619-01 TCGA-55-8621-01 TCGA-55-A4DF-01 TCGA-62-8397-01
#> 426 427 428 429 430
#> TCGA-62-A46O-01 TCGA-62-A46P-01 TCGA-62-A46Y-01 TCGA-64-5779-01 TCGA-64-5781-01
#> 431 432 433 434 435
#> TCGA-69-7760-01 TCGA-69-7761-01 TCGA-69-7763-01 TCGA-69-7764-01 TCGA-69-7979-01
#> 436 437 438 439 440
#> TCGA-69-8255-01 TCGA-69-A59K-01 TCGA-71-6725-01 TCGA-73-4659-01 TCGA-73-4668-01
#> 441 442 443 444 445
#> TCGA-73-4675-01 TCGA-75-5122-01 TCGA-75-5125-01 TCGA-75-6203-01 TCGA-75-6205-01
#> 446 447 448 449 450
#> TCGA-75-6207-01 TCGA-75-6212-01 TCGA-75-7025-01 TCGA-75-7031-01 TCGA-78-7154-01
#> 451 452 453 454 455
#> TCGA-78-7156-01 TCGA-78-7162-01 TCGA-78-7163-01 TCGA-78-7535-01 TCGA-78-7536-01
#> 456 457 458 459 460
#> TCGA-78-7542-01 TCGA-78-8648-01 TCGA-80-5611-01 TCGA-86-6562-01 TCGA-86-7701-01
#> 461 462 463 464 465
#> TCGA-86-7955-01 TCGA-86-8073-01 TCGA-86-8358-01 TCGA-86-8669-01 TCGA-86-8671-01
#> 466 467 468 469 470
#> TCGA-86-8672-01 TCGA-86-A4P8-01 TCGA-91-6831-01 TCGA-91-7771-01 TCGA-91-8496-01
#> 471 472 473 474 475
#> TCGA-91-8497-01 TCGA-91-8499-01 TCGA-91-A4BC-01 TCGA-93-A4JQ-01 TCGA-95-8039-01
#> 476 477 478 479 480
#> TCGA-95-8494-01 TCGA-97-7547-01 TCGA-97-7552-01 TCGA-97-8172-01 TCGA-97-8552-01
#> 481 482 483 484 485
#> TCGA-97-A4M2-01 TCGA-97-A4M6-01 TCGA-99-7458-01 TCGA-99-AA5R-01 TCGA-J2-8192-01
#> 486 487 488 489 490
#> TCGA-J2-A4AE-01 TCGA-L4-A4E6-01 TCGA-MP-A4T6-01 TCGA-MP-A4TC-01 TCGA-MP-A4TH-01
#> 491 492 493 494 495
#> TCGA-MP-A4TJ-01 TCGA-MP-A5C7-01 TCGA-NJ-A4YF-01 TCGA-NJ-A55A-01 TCGA-NJ-A7XG-01
#> 496 497 498 499 500
#> TCGA-O1-A52J-01 TCGA-S2-AA1A-01
#> 501 502
#>
#>
#> $alteration.blocks
#> $alteration.blocks$MUT
#> ARID1A ATM BRAF CDKN2A CMTR2 CTNNB1 EGFR KEAP1 KRAS MGA
#> 1 2 3 4 5 6 7 8 9 10
#> NF1 PIK3CA PTPRD PTPRT RB1 RBM10 SETBP1 SETD2 SMAD4 SMARCA4
#> 11 12 13 14 15 16 17 18 19 20
#> STK11 TP53 U2AF1
#> 21 22 23
#>
#>
#> $missing.samples
#> integer(0)
#>
#> $missing.alterations
#> integer(0)
#>
# }