| 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: | no |
| 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
- 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
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
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 and depletion is observed in controls.
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
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_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