Help for package RareComb

Title:

Combinatorial and Statistical Analyses of Rare Events

Version:

1.1

Description:

A custom implementation of the apriori algorithm and binomial tests to identify combinations of features (genes, variants etc) significantly enriched for simultaneous mutations/events from sparse Boolean input, see Vijay Kumar Pounraja, Santhosh Girirajan (2021). Version 1.1 includes a minor adjustment to the number of combinations to be considered for multiple testing correction. This updated version is more conservative in its approach and hence more selective. <doi:10.1101/2021.10.01.462832>.

License:

MIT + file LICENSE

Encoding:

UTF-8

LazyData:

true

Depends:

R (≥ 2.10)

Imports:

magrittr, arules, dplyr, methods, pwr, stringr, tidyr, reshape2, sqldf

RoxygenNote:

7.1.1

NeedsCompilation:

Packaged:

2022-02-24 00:30:38 UTC; Vijay

Author:

Vijay Kumar Pounraja

[aut, cre]

Maintainer:

Vijay Kumar Pounraja <vijaykumar.mp@gmail.com>

Repository:

CRAN

Date/Publication:

2022-02-24 01:00:02 UTC

Analyze relationships between rare events among multiple input and output variables

Description

This function takes a Boolean dataframe as input and analyzes the relationship between input and output variables for the combinations that that include at least a single output variable andmeet all the input criteria specified by the user.

Usage

analyze_in_out_simultaneity(boolean_input_mult_df, combo_length, min_output_count,
                            max_output_count, min_indv_threshold, max_freq_threshold,
                            input_format, output_format, pval_filter_threshold,
                            adj_pval_type)

Arguments

boolean_input_mult_df

An input Boolean dataframe with multiple input and outcome variables

combo_length

The length of the combinations specified by the user

min_output_count

Minimum number of output variables present in the combination

max_output_count

Maximum number of output variables present in the combination

min_indv_threshold

Minimum number of instances that support the combination

max_freq_threshold

Maximum fraction of the cohort size that could support a combination (i.e., filter out highly frequent events)

input_format

Optional | Naming convention used for input variables (Default = 'Input_')

output_format

Optional | Naming convention used for output variables (Default = 'Output_')

pval_filter_threshold

Optional | p-value cut-off to use to identify significant combinations (Default = 0.05)

adj_pval_type

Optional | Type of multiple testing corrections to use (Default = 'BH'; Alternative option = 'bonferroni')

Value

A dataframe with the list of multiple-testing adjusted statistically significant combinations along with quantitative measures (frequencies, p-values etc) that support the findings.

Author(s)

Vijay Kumar Pounraja

Examples

    analyze_in_out_simultaneity(boolean_input_mult_df, 3, 1, 2, 5, 0.25,
                                input_format = 'Input_', output_format = 'Output_',
                                pval_filter_threshold = 0.05, adj_pval_type = 'BH')

Sparse Boolean dataframe with rare variant information and a single outcome variable

Description

A synthetic dataset containing information about 5000 individuals (rows) and 1000 rare variants (columns).

Usage

boolean_input_df

Format

A data frame with 5000 rows and 1002 variables:

Sample_Name: Unique identifier of the samples
Input_1: Presence and absense of rare variant 1
Input_2: Presence and absense of rare variant 2
Input_3: Presence and absense of rare variant 3
Input_4: Presence and absense of rare variant 4
Input_5: Presence and absense of rare variant 5
Input_6: Presence and absense of rare variant 6
Input_7: Presence and absense of rare variant 7
Input_8: Presence and absense of rare variant 8
Input_9: Presence and absense of rare variant 9
Input_10: Presence and absense of rare variant 10
Input_11: Presence and absense of rare variant 11
Input_12: Presence and absense of rare variant 12
Input_13: Presence and absense of rare variant 13
Input_14: Presence and absense of rare variant 14
Input_15: Presence and absense of rare variant 15
Input_16: Presence and absense of rare variant 16
Input_17: Presence and absense of rare variant 17
Input_18: Presence and absense of rare variant 18
Input_19: Presence and absense of rare variant 19
Input_20: Presence and absense of rare variant 20
Input_21: Presence and absense of rare variant 21
Input_22: Presence and absense of rare variant 22
Input_23: Presence and absense of rare variant 23
Input_24: Presence and absense of rare variant 24
Input_25: Presence and absense of rare variant 25
Input_26: Presence and absense of rare variant 26
Input_27: Presence and absense of rare variant 27
Input_28: Presence and absense of rare variant 28
Input_29: Presence and absense of rare variant 29
Input_30: Presence and absense of rare variant 30
Input_31: Presence and absense of rare variant 31
Input_32: Presence and absense of rare variant 32
Input_33: Presence and absense of rare variant 33
Input_34: Presence and absense of rare variant 34
Input_35: Presence and absense of rare variant 35
Input_36: Presence and absense of rare variant 36
Input_37: Presence and absense of rare variant 37
Input_38: Presence and absense of rare variant 38
Input_39: Presence and absense of rare variant 39
Input_40: Presence and absense of rare variant 40
Input_41: Presence and absense of rare variant 41
Input_42: Presence and absense of rare variant 42
Input_43: Presence and absense of rare variant 43
Input_44: Presence and absense of rare variant 44
Input_45: Presence and absense of rare variant 45
Input_46: Presence and absense of rare variant 46
Input_47: Presence and absense of rare variant 47
Input_48: Presence and absense of rare variant 48
Input_49: Presence and absense of rare variant 49
Input_50: Presence and absense of rare variant 50
Input_51: Presence and absense of rare variant 51
Input_52: Presence and absense of rare variant 52
Input_53: Presence and absense of rare variant 53
Input_54: Presence and absense of rare variant 54
Input_55: Presence and absense of rare variant 55
Input_56: Presence and absense of rare variant 56
Input_57: Presence and absense of rare variant 57
Input_58: Presence and absense of rare variant 58
Input_59: Presence and absense of rare variant 59
Input_60: Presence and absense of rare variant 60
Input_61: Presence and absense of rare variant 61
Input_62: Presence and absense of rare variant 62
Input_63: Presence and absense of rare variant 63
Input_64: Presence and absense of rare variant 64
Input_65: Presence and absense of rare variant 65
Input_66: Presence and absense of rare variant 66
Input_67: Presence and absense of rare variant 67
Input_68: Presence and absense of rare variant 68
Input_69: Presence and absense of rare variant 69
Input_70: Presence and absense of rare variant 70
Input_71: Presence and absense of rare variant 71
Input_72: Presence and absense of rare variant 72
Input_73: Presence and absense of rare variant 73
Input_74: Presence and absense of rare variant 74
Input_75: Presence and absense of rare variant 75
Input_76: Presence and absense of rare variant 76
Input_77: Presence and absense of rare variant 77
Input_78: Presence and absense of rare variant 78
Input_79: Presence and absense of rare variant 79
Input_80: Presence and absense of rare variant 80
Input_81: Presence and absense of rare variant 81
Input_82: Presence and absense of rare variant 82
Input_83: Presence and absense of rare variant 83
Input_84: Presence and absense of rare variant 84
Input_85: Presence and absense of rare variant 85
Input_86: Presence and absense of rare variant 86
Input_87: Presence and absense of rare variant 87
Input_88: Presence and absense of rare variant 88
Input_89: Presence and absense of rare variant 89
Input_90: Presence and absense of rare variant 90
Input_91: Presence and absense of rare variant 91
Input_92: Presence and absense of rare variant 92
Input_93: Presence and absense of rare variant 93
Input_94: Presence and absense of rare variant 94
Input_95: Presence and absense of rare variant 95
Input_96: Presence and absense of rare variant 96
Input_97: Presence and absense of rare variant 97
Input_98: Presence and absense of rare variant 98
Input_99: Presence and absense of rare variant 99
Input_100: Presence and absense of rare variant 100
Input_101: Presence and absense of rare variant 101
Input_102: Presence and absense of rare variant 102
Input_103: Presence and absense of rare variant 103
Input_104: Presence and absense of rare variant 104
Input_105: Presence and absense of rare variant 105
Input_106: Presence and absense of rare variant 106
Input_107: Presence and absense of rare variant 107
Input_108: Presence and absense of rare variant 108
Input_109: Presence and absense of rare variant 109
Input_110: Presence and absense of rare variant 110
Input_111: Presence and absense of rare variant 111
Input_112: Presence and absense of rare variant 112
Input_113: Presence and absense of rare variant 113
Input_114: Presence and absense of rare variant 114
Input_115: Presence and absense of rare variant 115
Input_116: Presence and absense of rare variant 116
Input_117: Presence and absense of rare variant 117
Input_118: Presence and absense of rare variant 118
Input_119: Presence and absense of rare variant 119
Input_120: Presence and absense of rare variant 120
Input_121: Presence and absense of rare variant 121
Input_122: Presence and absense of rare variant 122
Input_123: Presence and absense of rare variant 123
Input_124: Presence and absense of rare variant 124
Input_125: Presence and absense of rare variant 125
Input_126: Presence and absense of rare variant 126
Input_127: Presence and absense of rare variant 127
Input_128: Presence and absense of rare variant 128
Input_129: Presence and absense of rare variant 129
Input_130: Presence and absense of rare variant 130
Input_131: Presence and absense of rare variant 131
Input_132: Presence and absense of rare variant 132
Input_133: Presence and absense of rare variant 133
Input_134: Presence and absense of rare variant 134
Input_135: Presence and absense of rare variant 135
Input_136: Presence and absense of rare variant 136
Input_137: Presence and absense of rare variant 137
Input_138: Presence and absense of rare variant 138
Input_139: Presence and absense of rare variant 139
Input_140: Presence and absense of rare variant 140
Input_141: Presence and absense of rare variant 141
Input_142: Presence and absense of rare variant 142
Input_143: Presence and absense of rare variant 143
Input_144: Presence and absense of rare variant 144
Input_145: Presence and absense of rare variant 145
Input_146: Presence and absense of rare variant 146
Input_147: Presence and absense of rare variant 147
Input_148: Presence and absense of rare variant 148
Input_149: Presence and absense of rare variant 149
Input_150: Presence and absense of rare variant 150
Input_151: Presence and absense of rare variant 151
Input_152: Presence and absense of rare variant 152
Input_153: Presence and absense of rare variant 153
Input_154: Presence and absense of rare variant 154
Input_155: Presence and absense of rare variant 155
Input_156: Presence and absense of rare variant 156
Input_157: Presence and absense of rare variant 157
Input_158: Presence and absense of rare variant 158
Input_159: Presence and absense of rare variant 159
Input_160: Presence and absense of rare variant 160
Input_161: Presence and absense of rare variant 161
Input_162: Presence and absense of rare variant 162
Input_163: Presence and absense of rare variant 163
Input_164: Presence and absense of rare variant 164
Input_165: Presence and absense of rare variant 165
Input_166: Presence and absense of rare variant 166
Input_167: Presence and absense of rare variant 167
Input_168: Presence and absense of rare variant 168
Input_169: Presence and absense of rare variant 169
Input_170: Presence and absense of rare variant 170
Input_171: Presence and absense of rare variant 171
Input_172: Presence and absense of rare variant 172
Input_173: Presence and absense of rare variant 173
Input_174: Presence and absense of rare variant 174
Input_175: Presence and absense of rare variant 175
Input_176: Presence and absense of rare variant 176
Input_177: Presence and absense of rare variant 177
Input_178: Presence and absense of rare variant 178
Input_179: Presence and absense of rare variant 179
Input_180: Presence and absense of rare variant 180
Input_181: Presence and absense of rare variant 181
Input_182: Presence and absense of rare variant 182
Input_183: Presence and absense of rare variant 183
Input_184: Presence and absense of rare variant 184
Input_185: Presence and absense of rare variant 185
Input_186: Presence and absense of rare variant 186
Input_187: Presence and absense of rare variant 187
Input_188: Presence and absense of rare variant 188
Input_189: Presence and absense of rare variant 189
Input_190: Presence and absense of rare variant 190
Input_191: Presence and absense of rare variant 191
Input_192: Presence and absense of rare variant 192
Input_193: Presence and absense of rare variant 193
Input_194: Presence and absense of rare variant 194
Input_195: Presence and absense of rare variant 195
Input_196: Presence and absense of rare variant 196
Input_197: Presence and absense of rare variant 197
Input_198: Presence and absense of rare variant 198
Input_199: Presence and absense of rare variant 199
Input_200: Presence and absense of rare variant 200
Input_201: Presence and absense of rare variant 201
Input_202: Presence and absense of rare variant 202
Input_203: Presence and absense of rare variant 203
Input_204: Presence and absense of rare variant 204
Input_205: Presence and absense of rare variant 205
Input_206: Presence and absense of rare variant 206
Input_207: Presence and absense of rare variant 207
Input_208: Presence and absense of rare variant 208
Input_209: Presence and absense of rare variant 209
Input_210: Presence and absense of rare variant 210
Input_211: Presence and absense of rare variant 211
Input_212: Presence and absense of rare variant 212
Input_213: Presence and absense of rare variant 213
Input_214: Presence and absense of rare variant 214
Input_215: Presence and absense of rare variant 215
Input_216: Presence and absense of rare variant 216
Input_217: Presence and absense of rare variant 217
Input_218: Presence and absense of rare variant 218
Input_219: Presence and absense of rare variant 219
Input_220: Presence and absense of rare variant 220
Input_221: Presence and absense of rare variant 221
Input_222: Presence and absense of rare variant 222
Input_223: Presence and absense of rare variant 223
Input_224: Presence and absense of rare variant 224
Input_225: Presence and absense of rare variant 225
Input_226: Presence and absense of rare variant 226
Input_227: Presence and absense of rare variant 227
Input_228: Presence and absense of rare variant 228
Input_229: Presence and absense of rare variant 229
Input_230: Presence and absense of rare variant 230
Input_231: Presence and absense of rare variant 231
Input_232: Presence and absense of rare variant 232
Input_233: Presence and absense of rare variant 233
Input_234: Presence and absense of rare variant 234
Input_235: Presence and absense of rare variant 235
Input_236: Presence and absense of rare variant 236
Input_237: Presence and absense of rare variant 237
Input_238: Presence and absense of rare variant 238
Input_239: Presence and absense of rare variant 239
Input_240: Presence and absense of rare variant 240
Input_241: Presence and absense of rare variant 241
Input_242: Presence and absense of rare variant 242
Input_243: Presence and absense of rare variant 243
Input_244: Presence and absense of rare variant 244
Input_245: Presence and absense of rare variant 245
Input_246: Presence and absense of rare variant 246
Input_247: Presence and absense of rare variant 247
Input_248: Presence and absense of rare variant 248
Input_249: Presence and absense of rare variant 249
Input_250: Presence and absense of rare variant 250
Input_251: Presence and absense of rare variant 251
Input_252: Presence and absense of rare variant 252
Input_253: Presence and absense of rare variant 253
Input_254: Presence and absense of rare variant 254
Input_255: Presence and absense of rare variant 255
Input_256: Presence and absense of rare variant 256
Input_257: Presence and absense of rare variant 257
Input_258: Presence and absense of rare variant 258
Input_259: Presence and absense of rare variant 259
Input_260: Presence and absense of rare variant 260
Input_261: Presence and absense of rare variant 261
Input_262: Presence and absense of rare variant 262
Input_263: Presence and absense of rare variant 263
Input_264: Presence and absense of rare variant 264
Input_265: Presence and absense of rare variant 265
Input_266: Presence and absense of rare variant 266
Input_267: Presence and absense of rare variant 267
Input_268: Presence and absense of rare variant 268
Input_269: Presence and absense of rare variant 269
Input_270: Presence and absense of rare variant 270
Input_271: Presence and absense of rare variant 271
Input_272: Presence and absense of rare variant 272
Input_273: Presence and absense of rare variant 273
Input_274: Presence and absense of rare variant 274
Input_275: Presence and absense of rare variant 275
Input_276: Presence and absense of rare variant 276
Input_277: Presence and absense of rare variant 277
Input_278: Presence and absense of rare variant 278
Input_279: Presence and absense of rare variant 279
Input_280: Presence and absense of rare variant 280
Input_281: Presence and absense of rare variant 281
Input_282: Presence and absense of rare variant 282
Input_283: Presence and absense of rare variant 283
Input_284: Presence and absense of rare variant 284
Input_285: Presence and absense of rare variant 285
Input_286: Presence and absense of rare variant 286
Input_287: Presence and absense of rare variant 287
Input_288: Presence and absense of rare variant 288
Input_289: Presence and absense of rare variant 289
Input_290: Presence and absense of rare variant 290
Input_291: Presence and absense of rare variant 291
Input_292: Presence and absense of rare variant 292
Input_293: Presence and absense of rare variant 293
Input_294: Presence and absense of rare variant 294
Input_295: Presence and absense of rare variant 295
Input_296: Presence and absense of rare variant 296
Input_297: Presence and absense of rare variant 297
Input_298: Presence and absense of rare variant 298
Input_299: Presence and absense of rare variant 299
Input_300: Presence and absense of rare variant 300
Input_301: Presence and absense of rare variant 301
Input_302: Presence and absense of rare variant 302
Input_303: Presence and absense of rare variant 303
Input_304: Presence and absense of rare variant 304
Input_305: Presence and absense of rare variant 305
Input_306: Presence and absense of rare variant 306
Input_307: Presence and absense of rare variant 307
Input_308: Presence and absense of rare variant 308
Input_309: Presence and absense of rare variant 309
Input_310: Presence and absense of rare variant 310
Input_311: Presence and absense of rare variant 311
Input_312: Presence and absense of rare variant 312
Input_313: Presence and absense of rare variant 313
Input_314: Presence and absense of rare variant 314
Input_315: Presence and absense of rare variant 315
Input_316: Presence and absense of rare variant 316
Input_317: Presence and absense of rare variant 317
Input_318: Presence and absense of rare variant 318
Input_319: Presence and absense of rare variant 319
Input_320: Presence and absense of rare variant 320
Input_321: Presence and absense of rare variant 321
Input_322: Presence and absense of rare variant 322
Input_323: Presence and absense of rare variant 323
Input_324: Presence and absense of rare variant 324
Input_325: Presence and absense of rare variant 325
Input_326: Presence and absense of rare variant 326
Input_327: Presence and absense of rare variant 327
Input_328: Presence and absense of rare variant 328
Input_329: Presence and absense of rare variant 329
Input_330: Presence and absense of rare variant 330
Input_331: Presence and absense of rare variant 331
Input_332: Presence and absense of rare variant 332
Input_333: Presence and absense of rare variant 333
Input_334: Presence and absense of rare variant 334
Input_335: Presence and absense of rare variant 335
Input_336: Presence and absense of rare variant 336
Input_337: Presence and absense of rare variant 337
Input_338: Presence and absense of rare variant 338
Input_339: Presence and absense of rare variant 339
Input_340: Presence and absense of rare variant 340
Input_341: Presence and absense of rare variant 341
Input_342: Presence and absense of rare variant 342
Input_343: Presence and absense of rare variant 343
Input_344: Presence and absense of rare variant 344
Input_345: Presence and absense of rare variant 345
Input_346: Presence and absense of rare variant 346
Input_347: Presence and absense of rare variant 347
Input_348: Presence and absense of rare variant 348
Input_349: Presence and absense of rare variant 349
Input_350: Presence and absense of rare variant 350
Input_351: Presence and absense of rare variant 351
Input_352: Presence and absense of rare variant 352
Input_353: Presence and absense of rare variant 353
Input_354: Presence and absense of rare variant 354
Input_355: Presence and absense of rare variant 355
Input_356: Presence and absense of rare variant 356
Input_357: Presence and absense of rare variant 357
Input_358: Presence and absense of rare variant 358
Input_359: Presence and absense of rare variant 359
Input_360: Presence and absense of rare variant 360
Input_361: Presence and absense of rare variant 361
Input_362: Presence and absense of rare variant 362
Input_363: Presence and absense of rare variant 363
Input_364: Presence and absense of rare variant 364
Input_365: Presence and absense of rare variant 365
Input_366: Presence and absense of rare variant 366
Input_367: Presence and absense of rare variant 367
Input_368: Presence and absense of rare variant 368
Input_369: Presence and absense of rare variant 369
Input_370: Presence and absense of rare variant 370
Input_371: Presence and absense of rare variant 371
Input_372: Presence and absense of rare variant 372
Input_373: Presence and absense of rare variant 373
Input_374: Presence and absense of rare variant 374
Input_375: Presence and absense of rare variant 375
Input_376: Presence and absense of rare variant 376
Input_377: Presence and absense of rare variant 377
Input_378: Presence and absense of rare variant 378
Input_379: Presence and absense of rare variant 379
Input_380: Presence and absense of rare variant 380
Input_381: Presence and absense of rare variant 381
Input_382: Presence and absense of rare variant 382
Input_383: Presence and absense of rare variant 383
Input_384: Presence and absense of rare variant 384
Input_385: Presence and absense of rare variant 385
Input_386: Presence and absense of rare variant 386
Input_387: Presence and absense of rare variant 387
Input_388: Presence and absense of rare variant 388
Input_389: Presence and absense of rare variant 389
Input_390: Presence and absense of rare variant 390
Input_391: Presence and absense of rare variant 391
Input_392: Presence and absense of rare variant 392
Input_393: Presence and absense of rare variant 393
Input_394: Presence and absense of rare variant 394
Input_395: Presence and absense of rare variant 395
Input_396: Presence and absense of rare variant 396
Input_397: Presence and absense of rare variant 397
Input_398: Presence and absense of rare variant 398
Input_399: Presence and absense of rare variant 399
Input_400: Presence and absense of rare variant 400
Input_401: Presence and absense of rare variant 401
Input_402: Presence and absense of rare variant 402
Input_403: Presence and absense of rare variant 403
Input_404: Presence and absense of rare variant 404
Input_405: Presence and absense of rare variant 405
Input_406: Presence and absense of rare variant 406
Input_407: Presence and absense of rare variant 407
Input_408: Presence and absense of rare variant 408
Input_409: Presence and absense of rare variant 409
Input_410: Presence and absense of rare variant 410
Input_411: Presence and absense of rare variant 411
Input_412: Presence and absense of rare variant 412
Input_413: Presence and absense of rare variant 413
Input_414: Presence and absense of rare variant 414
Input_415: Presence and absense of rare variant 415
Input_416: Presence and absense of rare variant 416
Input_417: Presence and absense of rare variant 417
Input_418: Presence and absense of rare variant 418
Input_419: Presence and absense of rare variant 419
Input_420: Presence and absense of rare variant 420
Input_421: Presence and absense of rare variant 421
Input_422: Presence and absense of rare variant 422
Input_423: Presence and absense of rare variant 423
Input_424: Presence and absense of rare variant 424
Input_425: Presence and absense of rare variant 425
Input_426: Presence and absense of rare variant 426
Input_427: Presence and absense of rare variant 427
Input_428: Presence and absense of rare variant 428
Input_429: Presence and absense of rare variant 429
Input_430: Presence and absense of rare variant 430
Input_431: Presence and absense of rare variant 431
Input_432: Presence and absense of rare variant 432
Input_433: Presence and absense of rare variant 433
Input_434: Presence and absense of rare variant 434
Input_435: Presence and absense of rare variant 435
Input_436: Presence and absense of rare variant 436
Input_437: Presence and absense of rare variant 437
Input_438: Presence and absense of rare variant 438
Input_439: Presence and absense of rare variant 439
Input_440: Presence and absense of rare variant 440
Input_441: Presence and absense of rare variant 441
Input_442: Presence and absense of rare variant 442
Input_443: Presence and absense of rare variant 443
Input_444: Presence and absense of rare variant 444
Input_445: Presence and absense of rare variant 445
Input_446: Presence and absense of rare variant 446
Input_447: Presence and absense of rare variant 447
Input_448: Presence and absense of rare variant 448
Input_449: Presence and absense of rare variant 449
Input_450: Presence and absense of rare variant 450
Input_451: Presence and absense of rare variant 451
Input_452: Presence and absense of rare variant 452
Input_453: Presence and absense of rare variant 453
Input_454: Presence and absense of rare variant 454
Input_455: Presence and absense of rare variant 455
Input_456: Presence and absense of rare variant 456
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Input_459: Presence and absense of rare variant 459
Input_460: Presence and absense of rare variant 460
Input_461: Presence and absense of rare variant 461
Input_462: Presence and absense of rare variant 462
Input_463: Presence and absense of rare variant 463
Input_464: Presence and absense of rare variant 464
Input_465: Presence and absense of rare variant 465
Input_466: Presence and absense of rare variant 466
Input_467: Presence and absense of rare variant 467
Input_468: Presence and absense of rare variant 468
Input_469: Presence and absense of rare variant 469
Input_470: Presence and absense of rare variant 470
Input_471: Presence and absense of rare variant 471
Input_472: Presence and absense of rare variant 472
Input_473: Presence and absense of rare variant 473
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Input_476: Presence and absense of rare variant 476
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Input_478: Presence and absense of rare variant 478
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Input_481: Presence and absense of rare variant 481
Input_482: Presence and absense of rare variant 482
Input_483: Presence and absense of rare variant 483
Input_484: Presence and absense of rare variant 484
Input_485: Presence and absense of rare variant 485
Input_486: Presence and absense of rare variant 486
Input_487: Presence and absense of rare variant 487
Input_488: Presence and absense of rare variant 488
Input_489: Presence and absense of rare variant 489
Input_490: Presence and absense of rare variant 490
Input_491: Presence and absense of rare variant 491
Input_492: Presence and absense of rare variant 492
Input_493: Presence and absense of rare variant 493
Input_494: Presence and absense of rare variant 494
Input_495: Presence and absense of rare variant 495
Input_496: Presence and absense of rare variant 496
Input_497: Presence and absense of rare variant 497
Input_498: Presence and absense of rare variant 498
Input_499: Presence and absense of rare variant 499
Input_500: Presence and absense of rare variant 500
Output_1: Disease outcome or phenotype

Sparse Boolean dataframe with rare variant information and multiple outcome variables

Description

A synthetic dataset containing information about 5000 individuals (rows) and 1000 rare variants (columns) and 3 outcome variables.

Usage

boolean_input_mult_df

Format

A data frame with 5000 rows and 1004 variables:

Sample_Name: Unique identifier of the samples
Input_1: Presence and absense of rare variant 1
Input_2: Presence and absense of rare variant 2
Input_3: Presence and absense of rare variant 3
Input_4: Presence and absense of rare variant 4
Input_5: Presence and absense of rare variant 5
Input_6: Presence and absense of rare variant 6
Input_7: Presence and absense of rare variant 7
Input_8: Presence and absense of rare variant 8
Input_9: Presence and absense of rare variant 9
Input_10: Presence and absense of rare variant 10
Input_11: Presence and absense of rare variant 11
Input_12: Presence and absense of rare variant 12
Input_13: Presence and absense of rare variant 13
Input_14: Presence and absense of rare variant 14
Input_15: Presence and absense of rare variant 15
Input_16: Presence and absense of rare variant 16
Input_17: Presence and absense of rare variant 17
Input_18: Presence and absense of rare variant 18
Input_19: Presence and absense of rare variant 19
Input_20: Presence and absense of rare variant 20
Input_21: Presence and absense of rare variant 21
Input_22: Presence and absense of rare variant 22
Input_23: Presence and absense of rare variant 23
Input_24: Presence and absense of rare variant 24
Input_25: Presence and absense of rare variant 25
Input_26: Presence and absense of rare variant 26
Input_27: Presence and absense of rare variant 27
Input_28: Presence and absense of rare variant 28
Input_29: Presence and absense of rare variant 29
Input_30: Presence and absense of rare variant 30
Input_31: Presence and absense of rare variant 31
Input_32: Presence and absense of rare variant 32
Input_33: Presence and absense of rare variant 33
Input_34: Presence and absense of rare variant 34
Input_35: Presence and absense of rare variant 35
Input_36: Presence and absense of rare variant 36
Input_37: Presence and absense of rare variant 37
Input_38: Presence and absense of rare variant 38
Input_39: Presence and absense of rare variant 39
Input_40: Presence and absense of rare variant 40
Input_41: Presence and absense of rare variant 41
Input_42: Presence and absense of rare variant 42
Input_43: Presence and absense of rare variant 43
Input_44: Presence and absense of rare variant 44
Input_45: Presence and absense of rare variant 45
Input_46: Presence and absense of rare variant 46
Input_47: Presence and absense of rare variant 47
Input_48: Presence and absense of rare variant 48
Input_49: Presence and absense of rare variant 49
Input_50: Presence and absense of rare variant 50
Input_51: Presence and absense of rare variant 51
Input_52: Presence and absense of rare variant 52
Input_53: Presence and absense of rare variant 53
Input_54: Presence and absense of rare variant 54
Input_55: Presence and absense of rare variant 55
Input_56: Presence and absense of rare variant 56
Input_57: Presence and absense of rare variant 57
Input_58: Presence and absense of rare variant 58
Input_59: Presence and absense of rare variant 59
Input_60: Presence and absense of rare variant 60
Input_61: Presence and absense of rare variant 61
Input_62: Presence and absense of rare variant 62
Input_63: Presence and absense of rare variant 63
Input_64: Presence and absense of rare variant 64
Input_65: Presence and absense of rare variant 65
Input_66: Presence and absense of rare variant 66
Input_67: Presence and absense of rare variant 67
Input_68: Presence and absense of rare variant 68
Input_69: Presence and absense of rare variant 69
Input_70: Presence and absense of rare variant 70
Input_71: Presence and absense of rare variant 71
Input_72: Presence and absense of rare variant 72
Input_73: Presence and absense of rare variant 73
Input_74: Presence and absense of rare variant 74
Input_75: Presence and absense of rare variant 75
Input_76: Presence and absense of rare variant 76
Input_77: Presence and absense of rare variant 77
Input_78: Presence and absense of rare variant 78
Input_79: Presence and absense of rare variant 79
Input_80: Presence and absense of rare variant 80
Input_81: Presence and absense of rare variant 81
Input_82: Presence and absense of rare variant 82
Input_83: Presence and absense of rare variant 83
Input_84: Presence and absense of rare variant 84
Input_85: Presence and absense of rare variant 85
Input_86: Presence and absense of rare variant 86
Input_87: Presence and absense of rare variant 87
Input_88: Presence and absense of rare variant 88
Input_89: Presence and absense of rare variant 89
Input_90: Presence and absense of rare variant 90
Input_91: Presence and absense of rare variant 91
Input_92: Presence and absense of rare variant 92
Input_93: Presence and absense of rare variant 93
Input_94: Presence and absense of rare variant 94
Input_95: Presence and absense of rare variant 95
Input_96: Presence and absense of rare variant 96
Input_97: Presence and absense of rare variant 97
Input_98: Presence and absense of rare variant 98
Input_99: Presence and absense of rare variant 99
Input_100: Presence and absense of rare variant 100
Input_101: Presence and absense of rare variant 101
Input_102: Presence and absense of rare variant 102
Input_103: Presence and absense of rare variant 103
Input_104: Presence and absense of rare variant 104
Input_105: Presence and absense of rare variant 105
Input_106: Presence and absense of rare variant 106
Input_107: Presence and absense of rare variant 107
Input_108: Presence and absense of rare variant 108
Input_109: Presence and absense of rare variant 109
Input_110: Presence and absense of rare variant 110
Input_111: Presence and absense of rare variant 111
Input_112: Presence and absense of rare variant 112
Input_113: Presence and absense of rare variant 113
Input_114: Presence and absense of rare variant 114
Input_115: Presence and absense of rare variant 115
Input_116: Presence and absense of rare variant 116
Input_117: Presence and absense of rare variant 117
Input_118: Presence and absense of rare variant 118
Input_119: Presence and absense of rare variant 119
Input_120: Presence and absense of rare variant 120
Input_121: Presence and absense of rare variant 121
Input_122: Presence and absense of rare variant 122
Input_123: Presence and absense of rare variant 123
Input_124: Presence and absense of rare variant 124
Input_125: Presence and absense of rare variant 125
Input_126: Presence and absense of rare variant 126
Input_127: Presence and absense of rare variant 127
Input_128: Presence and absense of rare variant 128
Input_129: Presence and absense of rare variant 129
Input_130: Presence and absense of rare variant 130
Input_131: Presence and absense of rare variant 131
Input_132: Presence and absense of rare variant 132
Input_133: Presence and absense of rare variant 133
Input_134: Presence and absense of rare variant 134
Input_135: Presence and absense of rare variant 135
Input_136: Presence and absense of rare variant 136
Input_137: Presence and absense of rare variant 137
Input_138: Presence and absense of rare variant 138
Input_139: Presence and absense of rare variant 139
Input_140: Presence and absense of rare variant 140
Input_141: Presence and absense of rare variant 141
Input_142: Presence and absense of rare variant 142
Input_143: Presence and absense of rare variant 143
Input_144: Presence and absense of rare variant 144
Input_145: Presence and absense of rare variant 145
Input_146: Presence and absense of rare variant 146
Input_147: Presence and absense of rare variant 147
Input_148: Presence and absense of rare variant 148
Input_149: Presence and absense of rare variant 149
Input_150: Presence and absense of rare variant 150
Input_151: Presence and absense of rare variant 151
Input_152: Presence and absense of rare variant 152
Input_153: Presence and absense of rare variant 153
Input_154: Presence and absense of rare variant 154
Input_155: Presence and absense of rare variant 155
Input_156: Presence and absense of rare variant 156
Input_157: Presence and absense of rare variant 157
Input_158: Presence and absense of rare variant 158
Input_159: Presence and absense of rare variant 159
Input_160: Presence and absense of rare variant 160
Input_161: Presence and absense of rare variant 161
Input_162: Presence and absense of rare variant 162
Input_163: Presence and absense of rare variant 163
Input_164: Presence and absense of rare variant 164
Input_165: Presence and absense of rare variant 165
Input_166: Presence and absense of rare variant 166
Input_167: Presence and absense of rare variant 167
Input_168: Presence and absense of rare variant 168
Input_169: Presence and absense of rare variant 169
Input_170: Presence and absense of rare variant 170
Input_171: Presence and absense of rare variant 171
Input_172: Presence and absense of rare variant 172
Input_173: Presence and absense of rare variant 173
Input_174: Presence and absense of rare variant 174
Input_175: Presence and absense of rare variant 175
Input_176: Presence and absense of rare variant 176
Input_177: Presence and absense of rare variant 177
Input_178: Presence and absense of rare variant 178
Input_179: Presence and absense of rare variant 179
Input_180: Presence and absense of rare variant 180
Input_181: Presence and absense of rare variant 181
Input_182: Presence and absense of rare variant 182
Input_183: Presence and absense of rare variant 183
Input_184: Presence and absense of rare variant 184
Input_185: Presence and absense of rare variant 185
Input_186: Presence and absense of rare variant 186
Input_187: Presence and absense of rare variant 187
Input_188: Presence and absense of rare variant 188
Input_189: Presence and absense of rare variant 189
Input_190: Presence and absense of rare variant 190
Input_191: Presence and absense of rare variant 191
Input_192: Presence and absense of rare variant 192
Input_193: Presence and absense of rare variant 193
Input_194: Presence and absense of rare variant 194
Input_195: Presence and absense of rare variant 195
Input_196: Presence and absense of rare variant 196
Input_197: Presence and absense of rare variant 197
Input_198: Presence and absense of rare variant 198
Input_199: Presence and absense of rare variant 199
Input_200: Presence and absense of rare variant 200
Input_201: Presence and absense of rare variant 201
Input_202: Presence and absense of rare variant 202
Input_203: Presence and absense of rare variant 203
Input_204: Presence and absense of rare variant 204
Input_205: Presence and absense of rare variant 205
Input_206: Presence and absense of rare variant 206
Input_207: Presence and absense of rare variant 207
Input_208: Presence and absense of rare variant 208
Input_209: Presence and absense of rare variant 209
Input_210: Presence and absense of rare variant 210
Input_211: Presence and absense of rare variant 211
Input_212: Presence and absense of rare variant 212
Input_213: Presence and absense of rare variant 213
Input_214: Presence and absense of rare variant 214
Input_215: Presence and absense of rare variant 215
Input_216: Presence and absense of rare variant 216
Input_217: Presence and absense of rare variant 217
Input_218: Presence and absense of rare variant 218
Input_219: Presence and absense of rare variant 219
Input_220: Presence and absense of rare variant 220
Input_221: Presence and absense of rare variant 221
Input_222: Presence and absense of rare variant 222
Input_223: Presence and absense of rare variant 223
Input_224: Presence and absense of rare variant 224
Input_225: Presence and absense of rare variant 225
Input_226: Presence and absense of rare variant 226
Input_227: Presence and absense of rare variant 227
Input_228: Presence and absense of rare variant 228
Input_229: Presence and absense of rare variant 229
Input_230: Presence and absense of rare variant 230
Input_231: Presence and absense of rare variant 231
Input_232: Presence and absense of rare variant 232
Input_233: Presence and absense of rare variant 233
Input_234: Presence and absense of rare variant 234
Input_235: Presence and absense of rare variant 235
Input_236: Presence and absense of rare variant 236
Input_237: Presence and absense of rare variant 237
Input_238: Presence and absense of rare variant 238
Input_239: Presence and absense of rare variant 239
Input_240: Presence and absense of rare variant 240
Input_241: Presence and absense of rare variant 241
Input_242: Presence and absense of rare variant 242
Input_243: Presence and absense of rare variant 243
Input_244: Presence and absense of rare variant 244
Input_245: Presence and absense of rare variant 245
Input_246: Presence and absense of rare variant 246
Input_247: Presence and absense of rare variant 247
Input_248: Presence and absense of rare variant 248
Input_249: Presence and absense of rare variant 249
Input_250: Presence and absense of rare variant 250
Input_251: Presence and absense of rare variant 251
Input_252: Presence and absense of rare variant 252
Input_253: Presence and absense of rare variant 253
Input_254: Presence and absense of rare variant 254
Input_255: Presence and absense of rare variant 255
Input_256: Presence and absense of rare variant 256
Input_257: Presence and absense of rare variant 257
Input_258: Presence and absense of rare variant 258
Input_259: Presence and absense of rare variant 259
Input_260: Presence and absense of rare variant 260
Input_261: Presence and absense of rare variant 261
Input_262: Presence and absense of rare variant 262
Input_263: Presence and absense of rare variant 263
Input_264: Presence and absense of rare variant 264
Input_265: Presence and absense of rare variant 265
Input_266: Presence and absense of rare variant 266
Input_267: Presence and absense of rare variant 267
Input_268: Presence and absense of rare variant 268
Input_269: Presence and absense of rare variant 269
Input_270: Presence and absense of rare variant 270
Input_271: Presence and absense of rare variant 271
Input_272: Presence and absense of rare variant 272
Input_273: Presence and absense of rare variant 273
Input_274: Presence and absense of rare variant 274
Input_275: Presence and absense of rare variant 275
Input_276: Presence and absense of rare variant 276
Input_277: Presence and absense of rare variant 277
Input_278: Presence and absense of rare variant 278
Input_279: Presence and absense of rare variant 279
Input_280: Presence and absense of rare variant 280
Input_281: Presence and absense of rare variant 281
Input_282: Presence and absense of rare variant 282
Input_283: Presence and absense of rare variant 283
Input_284: Presence and absense of rare variant 284
Input_285: Presence and absense of rare variant 285
Input_286: Presence and absense of rare variant 286
Input_287: Presence and absense of rare variant 287
Input_288: Presence and absense of rare variant 288
Input_289: Presence and absense of rare variant 289
Input_290: Presence and absense of rare variant 290
Input_291: Presence and absense of rare variant 291
Input_292: Presence and absense of rare variant 292
Input_293: Presence and absense of rare variant 293
Input_294: Presence and absense of rare variant 294
Input_295: Presence and absense of rare variant 295
Input_296: Presence and absense of rare variant 296
Input_297: Presence and absense of rare variant 297
Input_298: Presence and absense of rare variant 298
Input_299: Presence and absense of rare variant 299
Input_300: Presence and absense of rare variant 300
Input_301: Presence and absense of rare variant 301
Input_302: Presence and absense of rare variant 302
Input_303: Presence and absense of rare variant 303
Input_304: Presence and absense of rare variant 304
Input_305: Presence and absense of rare variant 305
Input_306: Presence and absense of rare variant 306
Input_307: Presence and absense of rare variant 307
Input_308: Presence and absense of rare variant 308
Input_309: Presence and absense of rare variant 309
Input_310: Presence and absense of rare variant 310
Input_311: Presence and absense of rare variant 311
Input_312: Presence and absense of rare variant 312
Input_313: Presence and absense of rare variant 313
Input_314: Presence and absense of rare variant 314
Input_315: Presence and absense of rare variant 315
Input_316: Presence and absense of rare variant 316
Input_317: Presence and absense of rare variant 317
Input_318: Presence and absense of rare variant 318
Input_319: Presence and absense of rare variant 319
Input_320: Presence and absense of rare variant 320
Input_321: Presence and absense of rare variant 321
Input_322: Presence and absense of rare variant 322
Input_323: Presence and absense of rare variant 323
Input_324: Presence and absense of rare variant 324
Input_325: Presence and absense of rare variant 325
Input_326: Presence and absense of rare variant 326
Input_327: Presence and absense of rare variant 327
Input_328: Presence and absense of rare variant 328
Input_329: Presence and absense of rare variant 329
Input_330: Presence and absense of rare variant 330
Input_331: Presence and absense of rare variant 331
Input_332: Presence and absense of rare variant 332
Input_333: Presence and absense of rare variant 333
Input_334: Presence and absense of rare variant 334
Input_335: Presence and absense of rare variant 335
Input_336: Presence and absense of rare variant 336
Input_337: Presence and absense of rare variant 337
Input_338: Presence and absense of rare variant 338
Input_339: Presence and absense of rare variant 339
Input_340: Presence and absense of rare variant 340
Input_341: Presence and absense of rare variant 341
Input_342: Presence and absense of rare variant 342
Input_343: Presence and absense of rare variant 343
Input_344: Presence and absense of rare variant 344
Input_345: Presence and absense of rare variant 345
Input_346: Presence and absense of rare variant 346
Input_347: Presence and absense of rare variant 347
Input_348: Presence and absense of rare variant 348
Input_349: Presence and absense of rare variant 349
Input_350: Presence and absense of rare variant 350
Input_351: Presence and absense of rare variant 351
Input_352: Presence and absense of rare variant 352
Input_353: Presence and absense of rare variant 353
Input_354: Presence and absense of rare variant 354
Input_355: Presence and absense of rare variant 355
Input_356: Presence and absense of rare variant 356
Input_357: Presence and absense of rare variant 357
Input_358: Presence and absense of rare variant 358
Input_359: Presence and absense of rare variant 359
Input_360: Presence and absense of rare variant 360
Input_361: Presence and absense of rare variant 361
Input_362: Presence and absense of rare variant 362
Input_363: Presence and absense of rare variant 363
Input_364: Presence and absense of rare variant 364
Input_365: Presence and absense of rare variant 365
Input_366: Presence and absense of rare variant 366
Input_367: Presence and absense of rare variant 367
Input_368: Presence and absense of rare variant 368
Input_369: Presence and absense of rare variant 369
Input_370: Presence and absense of rare variant 370
Input_371: Presence and absense of rare variant 371
Input_372: Presence and absense of rare variant 372
Input_373: Presence and absense of rare variant 373
Input_374: Presence and absense of rare variant 374
Input_375: Presence and absense of rare variant 375
Input_376: Presence and absense of rare variant 376
Input_377: Presence and absense of rare variant 377
Input_378: Presence and absense of rare variant 378
Input_379: Presence and absense of rare variant 379
Input_380: Presence and absense of rare variant 380
Input_381: Presence and absense of rare variant 381
Input_382: Presence and absense of rare variant 382
Input_383: Presence and absense of rare variant 383
Input_384: Presence and absense of rare variant 384
Input_385: Presence and absense of rare variant 385
Input_386: Presence and absense of rare variant 386
Input_387: Presence and absense of rare variant 387
Input_388: Presence and absense of rare variant 388
Input_389: Presence and absense of rare variant 389
Input_390: Presence and absense of rare variant 390
Input_391: Presence and absense of rare variant 391
Input_392: Presence and absense of rare variant 392
Input_393: Presence and absense of rare variant 393
Input_394: Presence and absense of rare variant 394
Input_395: Presence and absense of rare variant 395
Input_396: Presence and absense of rare variant 396
Input_397: Presence and absense of rare variant 397
Input_398: Presence and absense of rare variant 398
Input_399: Presence and absense of rare variant 399
Input_400: Presence and absense of rare variant 400
Input_401: Presence and absense of rare variant 401
Input_402: Presence and absense of rare variant 402
Input_403: Presence and absense of rare variant 403
Input_404: Presence and absense of rare variant 404
Input_405: Presence and absense of rare variant 405
Input_406: Presence and absense of rare variant 406
Input_407: Presence and absense of rare variant 407
Input_408: Presence and absense of rare variant 408
Input_409: Presence and absense of rare variant 409
Input_410: Presence and absense of rare variant 410
Input_411: Presence and absense of rare variant 411
Input_412: Presence and absense of rare variant 412
Input_413: Presence and absense of rare variant 413
Input_414: Presence and absense of rare variant 414
Input_415: Presence and absense of rare variant 415
Input_416: Presence and absense of rare variant 416
Input_417: Presence and absense of rare variant 417
Input_418: Presence and absense of rare variant 418
Input_419: Presence and absense of rare variant 419
Input_420: Presence and absense of rare variant 420
Input_421: Presence and absense of rare variant 421
Input_422: Presence and absense of rare variant 422
Input_423: Presence and absense of rare variant 423
Input_424: Presence and absense of rare variant 424
Input_425: Presence and absense of rare variant 425
Input_426: Presence and absense of rare variant 426
Input_427: Presence and absense of rare variant 427
Input_428: Presence and absense of rare variant 428
Input_429: Presence and absense of rare variant 429
Input_430: Presence and absense of rare variant 430
Input_431: Presence and absense of rare variant 431
Input_432: Presence and absense of rare variant 432
Input_433: Presence and absense of rare variant 433
Input_434: Presence and absense of rare variant 434
Input_435: Presence and absense of rare variant 435
Input_436: Presence and absense of rare variant 436
Input_437: Presence and absense of rare variant 437
Input_438: Presence and absense of rare variant 438
Input_439: Presence and absense of rare variant 439
Input_440: Presence and absense of rare variant 440
Input_441: Presence and absense of rare variant 441
Input_442: Presence and absense of rare variant 442
Input_443: Presence and absense of rare variant 443
Input_444: Presence and absense of rare variant 444
Input_445: Presence and absense of rare variant 445
Input_446: Presence and absense of rare variant 446
Input_447: Presence and absense of rare variant 447
Input_448: Presence and absense of rare variant 448
Input_449: Presence and absense of rare variant 449
Input_450: Presence and absense of rare variant 450
Input_451: Presence and absense of rare variant 451
Input_452: Presence and absense of rare variant 452
Input_453: Presence and absense of rare variant 453
Input_454: Presence and absense of rare variant 454
Input_455: Presence and absense of rare variant 455
Input_456: Presence and absense of rare variant 456
Input_457: Presence and absense of rare variant 457
Input_458: Presence and absense of rare variant 458
Input_459: Presence and absense of rare variant 459
Input_460: Presence and absense of rare variant 460
Input_461: Presence and absense of rare variant 461
Input_462: Presence and absense of rare variant 462
Input_463: Presence and absense of rare variant 463
Input_464: Presence and absense of rare variant 464
Input_465: Presence and absense of rare variant 465
Input_466: Presence and absense of rare variant 466
Input_467: Presence and absense of rare variant 467
Input_468: Presence and absense of rare variant 468
Input_469: Presence and absense of rare variant 469
Input_470: Presence and absense of rare variant 470
Input_471: Presence and absense of rare variant 471
Input_472: Presence and absense of rare variant 472
Input_473: Presence and absense of rare variant 473
Input_474: Presence and absense of rare variant 474
Input_475: Presence and absense of rare variant 475
Input_476: Presence and absense of rare variant 476
Input_477: Presence and absense of rare variant 477
Input_478: Presence and absense of rare variant 478
Input_479: Presence and absense of rare variant 479
Input_480: Presence and absense of rare variant 480
Input_481: Presence and absense of rare variant 481
Input_482: Presence and absense of rare variant 482
Input_483: Presence and absense of rare variant 483
Input_484: Presence and absense of rare variant 484
Input_485: Presence and absense of rare variant 485
Input_486: Presence and absense of rare variant 486
Input_487: Presence and absense of rare variant 487
Input_488: Presence and absense of rare variant 488
Input_489: Presence and absense of rare variant 489
Input_490: Presence and absense of rare variant 490
Input_491: Presence and absense of rare variant 491
Input_492: Presence and absense of rare variant 492
Input_493: Presence and absense of rare variant 493
Input_494: Presence and absense of rare variant 494
Input_495: Presence and absense of rare variant 495
Input_496: Presence and absense of rare variant 496
Input_497: Presence and absense of rare variant 497
Input_498: Presence and absense of rare variant 498
Input_499: Presence and absense of rare variant 499
Input_500: Presence and absense of rare variant 500
Output_1: Disease outcome or phenotype 1
Output_2: Disease outcome or phenotype 2
Output_3: Disease outcome or phenotype 3

Compare the enrichment in combinations of input variables between the binary outcomes (case/control)

Description

This function takes a Boolean dataframe as input and quantifies the enrichment in the observed frequency of combinations that meet the criteria specified by the users compared to their corresponding expectation derived under the assumption of independence between the constituent elements of each combination. The function then reports the multiple-testing adjusted significant combinations in which enrichment is observed in cases but not in controls.

Usage

compare_enrichment(boolean_input_df, combo_length, min_indv_threshold,
                   max_freq_threshold, input_format, output_format,
                   pval_filter_threshold, adj_pval_type, min_power_threshold,
                   sample_names_ind)

Arguments

boolean_input_df

An input Boolean dataframe with multiple input and a single binary outcome variable

combo_length

The length of the combinations specified by the user

min_indv_threshold

Minimum number of instances that support the combination

max_freq_threshold

Maximum fraction of the cohort size that could support a combination (i.e., filter out highly frequent events)

input_format

Optional | Naming convention used for input variables (Default = 'Input_')

output_format

Optional | Naming convention used for output variables (Default = 'Output_')

pval_filter_threshold

Optional | p-value cut-off to use to identify significant combinations in cases (Default = 0.05)

adj_pval_type

Optional | Type of multiple testing corrections to use (Default = 'BH'; Alternative option = 'bonferroni')

min_power_threshold

Optional | Minimum statistical power (at 5% sig.threshold) required for significant combinations to be returned in the results (Default = 0.7)

sample_names_ind

Optional | Indicator to specify if the output should includes row names that support each significant combination (Default = 'N'; Alternative option = 'Y')

Value

A dataframe with the list of multiple-testing adjusted statistically significant combinations along with quantitative measures (frequencies, p-values etc) that support the findings.

Author(s)

Vijay Kumar Pounraja

Examples



   compare_enrichment(boolean_input_df, 3, 5, 0.25, input_format = 'Input_',
                      output_format = 'Output_', adj_pval_type = 'bonferroni',
                      sample_names_ind = 'N')

Compare the enrichment in combinations of input variables between the binary outcomes (case/control)

Description

Usage

compare_enrichment_depletion(boolean_input_df, combo_length, min_indv_threshold,
                             max_freq_threshold, input_format, output_format,
                             pval_filter_threshold, adj_pval_type, min_power_threshold,
                             sample_names_ind)

Arguments

boolean_input_df

An input Boolean dataframe with multiple input and a single binary outcome variable

combo_length

The length of the combinations specified by the user

min_indv_threshold

Minimum number of instances that support the combination

max_freq_threshold

Maximum fraction of the cohort size that could support a combination (i.e., filter out highly frequent events)

input_format

Optional | Naming convention used for input variables (Default = 'Input_')

output_format

Optional | Naming convention used for output variables (Default = 'Output_')

pval_filter_threshold

Optional | p-value cut-off to use to identify significant combinations in cases (Default = 0.05)

adj_pval_type

Optional | Type of multiple testing corrections to use (Default = 'BH'; Alternative option = 'bonferroni')

min_power_threshold

Optional | Minimum statistical power (at 5% sig.threshold) required for significant combinations to be returned in the results (Default = 0.7)

sample_names_ind

Optional | Indicator to specify if the output should includes row names that support each significant combination (Default = 'N'; Alternative option = 'Y')

Value

A dataframe with the list of multiple-testing adjusted statistically significant combinations along with quantitative measures (frequencies, p-values etc) that support the findings.

Author(s)

Vijay Kumar Pounraja

Examples


   compare_enrichment_depletion(boolean_input_df, 3, 5, 0.25, input_format = 'Input_',
                                output_format = 'Output_', adj_pval_type = 'bonferroni',
                                sample_names_ind = 'N')

Compare the enrichment in combinations of input variables between the binary outcomes (case/control)

Description

This function takes a Boolean dataframe as input and quantifies the enrichment in the observed frequency of combinations that include at least one of the input variables supplied by the user as well as meet other user-specified criteria compared to their corresponding expectation derived under the assumption of independence between the constituent elements of each combination. The function then reports the combinations in which enrichment is observed in cases but not in controls.

Usage

compare_enrichment_modifiers(boolean_input_df, combo_length, min_indv_threshold,
                             max_freq_threshold, primary_input_entities, input_format,
                             output_format, pval_filter_threshold, adj_pval_type,
                             min_power_threshold, sample_names_ind)

Arguments

boolean_input_df

An input Boolean dataframe with multiple input and a single binary outcome variable

combo_length

The length of the combinations specified by the user

min_indv_threshold

Minimum number of instances that support the combination

max_freq_threshold

Maximum fraction of the cohort size that could support a combination (i.e., filter out highly frequent events)

primary_input_entities

List of variables that MUST be part of the combinations identified by the method

input_format

Optional | Naming convention used for input variables (Default = 'Input_')

output_format

Optional | Naming convention used for output variables (Default = 'Output_')

pval_filter_threshold

Optional | p-value cut-off to use to identify significant combinations in cases (Default = 0.05)

adj_pval_type

Optional | Type of multiple testing corrections to use (Default = 'BH'; Alternative option = 'bonferroni')

min_power_threshold

Optional | Minimum statistical power (at 5% sig.threshold) required for significant combinations to be returned in the results (Default = 0.7)

sample_names_ind

Optional | Indicator to specify if the output should includes row names that support each significant combination (Default = 'N'; Alternative option = 'Y')

Value

A dataframe with the list of multiple-testing adjusted statistically significant combinations along with quantitative measures (frequencies, p-values etc) that support the findings.

Author(s)

Vijay Kumar Pounraja

Examples



   compare_enrichment_modifiers(boolean_input_df, 2, 4, 0.25, input_format = 'Input_',
                                output_format = 'Output_', primary_input_entities = input_list,
                                adj_pval_type = 'bonferroni', sample_names_ind = 'N')

Compare the observed frequencies of combinations with their expected frequencies under the assumption of independence within a single group

Description

This function takes a Boolean dataframe as input and compares the observed frequency of combinations that meet the criteria specified by the users with their corresponding expectation derived under the assumption of independence between the constituent elements of each combination

Usage

compare_expected_vs_observed(boolean_input_df, combo_length, min_indv_threshold,
                             max_freq_threshold, input_format,
                             pval_filter_threshold, adj_pval_type)

Arguments

boolean_input_df

An input Boolean dataframe with multiple input variables

combo_length

The length of the combinations specified by the user

min_indv_threshold

Minimum number of instances that support the combination

max_freq_threshold

Maximum fraction of the cohort size that could support a combination (i.e., filter out highly frequent events)

input_format

Optional | Naming convention used for input variables (Default = 'Input_')

pval_filter_threshold

Optional | p-value cut-off to use for multiple testing adjustment (Default = 0.05)

adj_pval_type

Optional | Type of multiple testing corrections to use (Default = 'BH'; Alternative option = 'bonferroni')

Value

A dataframe with the list of multiple-testing adjusted statistically significant combinations along with quantitative measures (frequencies, p-values etc) that support the findings.

Author(s)

Vijay Kumar Pounraja

Examples


   compare_expected_vs_observed(boolean_input_df, 2, 10, 0.25, 0.05,
                                input_format = 'Input_', adj_pval_type = 'BH')

Perform successive left joins to fetch information about the constituent elements of the combinations

Description

Fetching the frequency of multiple individual elements that make up the combinations of varying length and hence varying variable names or to join two similar data frames using identical variable names necessitates this function that supplements and joins data based on the length of the combinations.

Usage

custom_left_join(
  left_df,
  right_df,
  combo_length = combo_length,
  diff_colnames = diff_colnames
)

Arguments

left_df

The data frame with information about the combinations

right_df

The data frame with information either about the combinations or their constituent elements

combo_length

The length of the combinations specified by the user used to determine the number of successive joins to attempt

diff_colnames

Indicator that specifies if the joins are to be made based on same or different column names

Value

An output dataframe with the results of the join operation

Author(s)

Vijay Kumar Pounraja

A list of 50 random input variables

Description

A list of 50 random input variables

Usage

input_list

Format

A list of 50 random input variables:

Generate frequent items using the apriori algorithm

Description

This function takes in a factorized Boolean matrix and generate frequent itemsets that meet all the user provided criteria provided by the calling function.

Usage

run_apriori_freqitems(
  apriori_input_df,
  combo_length,
  support_threshold,
  input_colname_list,
  confidence_threshold = confidence_threshold,
  include_output_ind = include_output_ind,
  output_colname_list = output_colname_list
)

Arguments

apriori_input_df

An input factorized Boolean dataframe with multiple input and outcome variables

combo_length

The length of the combinations specified by the user

support_threshold

Minimum support value calculated based on the minimum absolute observed frequency threshold specified by the user

input_colname_list

A list of column names that identify the input variables

confidence_threshold

Minimum confidence threshold specified by the user

include_output_ind

Specifies if the outcome variables must also be made part of the analysis using the algorithm

output_colname_list

A list of column names that identify the outcome variables

Details

This is a function leveraged by few of the four main methods available to the users.

Value

A list of frequent item sets that meet all the constraints supplied to the apriori algorithm

Author(s)

Vijay Kumar Pounraja

Generate rules using the apriori algorithm

Description

This function takes in a factorized Boolean matrix and generate rules that meet all the user provided criteria while restricting the RHS of the rule based on the list of variables allowed in RHS provided by the calling function.

Usage

run_apriori_rules(
  apriori_input_df,
  combo_length,
  support_threshold,
  input_colname_list,
  confidence_threshold = confidence_threshold,
  output_colname_list = output_colname_list
)

Arguments

apriori_input_df

An input factorized Boolean dataframe with multiple input and outcome variables

combo_length

The length of the combinations specified by the user

support_threshold

Minimum support value calculated based on the minimum absolute observed frequency threshold specified by the user

input_colname_list

A list of column names that identify the input variables

confidence_threshold

Minimum confidence threshold specified by the user

output_colname_list

Optional | A list of column names that identify the outcome variables

Details

This is a function leveraged by few of the four main methods available to the users.

Value

A list of rules that meet all the constraints supplied to the apriori algorithm

Author(s)

Vijay Kumar Pounraja

Generate rules using the apriori algorithm

Description

This function takes in a factorized Boolean matrix and generate rules that meet all the user provided criteria while allowing the outcome variables to be part of either LHS or RHS of the rules but restricting the input variables to the LHS of the rules.

Usage

run_apriori_rules_inout_simult(
  apriori_input_df,
  combo_length,
  support_threshold,
  input_colname_list,
  output_colname_list = output_colname_list
)

Arguments

apriori_input_df

An input factorized Boolean dataframe with multiple input and outcome variables

combo_length

The length of the combinations specified by the user

support_threshold

Minimum support value calculated based on the minimum absolute observed frequency threshold specified by the user

input_colname_list

A list of column names that identify the input variables

output_colname_list

Optional | A list of column names that identify the outcome variables

Details

This is a function leveraged by few of the four main methods available to the users.

Value

A list of rules that meet all the constraints supplied to the apriori algorithm

Author(s)

Vijay Kumar Pounraja

Generate rules using the apriori algorithm

Description

Usage

run_apriori_rules_modifiers(
  apriori_input_df,
  combo_length,
  support_threshold,
  input_colname_list,
  output_colname_list = output_colname_list
)

Arguments

apriori_input_df

An input factorized Boolean dataframe with multiple input and outcome variables

combo_length

The length of the combinations specified by the user

support_threshold

Minimum support value calculated based on the minimum absolute observed frequency threshold specified by the user

input_colname_list

A list of column names that identify the input variables

output_colname_list

Optional | A list of column names that identify the outcome variables

Details

This is a function leveraged by few of the four main methods available to the users.

Value

A list of rules that meet all the constraints supplied to the apriori algorithm

Author(s)

Vijay Kumar Pounraja

Generate frequent items along with the names of supporting observations using the apriori algorithm

Description

This function takes in a factorized Boolean matrix and generate frequent item sets that meet all the user provided criteria provided by the calling function. This function includes in it's output the identifiers of observations that support each significant combination.

Usage

run_apriori_w_sample_names(
  apriori_input_df,
  combo_length,
  support_threshold,
  input_colname_list,
  input_sample_list,
  confidence_threshold = confidence_threshold,
  include_output_ind = include_output_ind,
  output_colname_list = output_colname_list
)

Arguments

apriori_input_df

An input factorized Boolean dataframe with multiple input and outcome variables

combo_length

The length of the combinations specified by the user

support_threshold

Minimum support value calculated based on the minimum absolute observed frequency threshold specified by the user

input_colname_list

A list of column names that identify the input variables

input_sample_list

A list of row names that identify the samples/observations

confidence_threshold

Minimum confidence threshold specified by the user

include_output_ind

Specifies if the outcome variables must also be made part of the analysis using the algorithm

output_colname_list

A list of column names that identify the outcome variables

Details

This is a function leveraged by few of the four main methods available to the users.

Value

A list of frequent item sets that meet all the constraints supplied to the apriori algorithm

Author(s)

Vijay Kumar Pounraja