Remove missing outcome values

rm_missing_outcome(dataset, outcome_colname)

Arguments

dataset

Dataframe with an outcome variable and other columns as features.

outcome_colname

Column name as a string of the outcome variable (default NULL; will be chosen automatically).

Value

dataset with no missing outcomes

Author

Zena Lapp, zenalapp@umich.edu

Examples

rm_missing_outcome(mikropml::otu_mini, "dx")
#> dx Otu00001 Otu00002 Otu00003 #> 1 normal 350 268 213 #> 2 normal 568 1320 13 #> 3 normal 151 756 802 #> 4 normal 299 30 1018 #> 5 normal 1409 174 0 #> 6 normal 167 712 213 #> 7 cancer 108 120 160 #> 8 normal 347 130 131 #> 9 normal 256 995 871 #> 10 cancer 1648 144 22 #> 11 normal 843 0 0 #> 12 normal 1404 386 103 #> 13 normal 230 226 152 #> 14 normal 86 426 123 #> 15 cancer 93 540 178 #> 16 cancer 1668 20 3 #> 17 normal 381 357 315 #> 18 normal 788 558 453 #> 19 normal 282 331 250 #> 20 normal 1245 24 71 #> 21 normal 2036 21 5 #> 22 normal 1046 40 71 #> 23 cancer 322 173 419 #> 24 normal 118 1132 582 #> 25 cancer 1976 563 193 #> 26 normal 1484 327 166 #> 27 normal 7 25 8 #> 28 cancer 115 67 139 #> 29 normal 287 87 118 #> 30 normal 31 179 58 #> 31 normal 878 866 783 #> 32 normal 287 670 99 #> 33 normal 1491 74 280 #> 34 normal 587 515 162 #> 35 normal 483 1564 834 #> 36 normal 660 31 44 #> 37 normal 422 230 192 #> 38 normal 526 1172 952 #> 39 normal 166 313 182 #> 40 normal 366 317 178 #> 41 normal 641 126 170 #> 42 normal 356 369 130 #> 43 normal 1636 15 7 #> 44 normal 308 68 131 #> 45 normal 905 160 53 #> 46 normal 1777 69 64 #> 47 normal 262 235 376 #> 48 normal 1758 36 51 #> 49 normal 45 343 131 #> 50 normal 1057 463 150 #> 51 normal 62 46 122 #> 52 normal 517 560 32 #> 53 cancer 1797 92 42 #> 54 normal 1513 140 1 #> 55 cancer 99 350 229 #> 56 cancer 2072 62 54 #> 57 normal 193 210 32 #> 58 normal 387 5041 5 #> 59 normal 335 1112 2 #> 60 normal 356 129 188 #> 61 normal 454 1967 5 #> 62 normal 1063 410 64 #> 63 normal 478 158 101 #> 64 normal 64 201 146 #> 65 normal 26 91 130 #> 66 normal 222 0 757 #> 67 normal 20 42 48 #> 68 normal 136 812 229 #> 69 normal 141 0 1283 #> 70 normal 571 2 527 #> 71 normal 453 73 565 #> 72 normal 141 465 658 #> 73 cancer 296 644 320 #> 74 normal 256 165 83 #> 75 normal 152 548 158 #> 76 cancer 931 87 376 #> 77 cancer 196 547 534 #> 78 normal 1089 356 1284 #> 79 normal 130 283 121 #> 80 normal 2380 2 16 #> 81 cancer 38 208 104 #> 82 normal 361 1262 226 #> 83 normal 1334 158 128 #> 84 cancer 66 92 2 #> 85 normal 81 188 1051 #> 86 cancer 166 91 428 #> 87 normal 636 474 412 #> 88 normal 191 1110 1 #> 89 cancer 332 805 546 #> 90 normal 542 2 559 #> 91 normal 93 984 517 #> 92 cancer 329 447 257 #> 93 cancer 1583 68 0 #> 94 cancer 174 149 79 #> 95 normal 497 488 143 #> 96 cancer 401 1530 1327 #> 97 cancer 787 11 4 #> 98 cancer 229 475 286 #> 99 cancer 1697 9 20 #> 100 normal 247 22 9 #> 101 normal 477 289 94 #> 102 cancer 2474 20 12 #> 103 cancer 1216 70 103 #> 104 normal 852 298 470 #> 105 normal 250 873 112 #> 106 normal 475 569 149 #> 107 cancer 129 236 2 #> 108 cancer 388 1079 572 #> 109 cancer 1683 21 38 #> 110 cancer 223 144 63 #> 111 normal 446 1182 520 #> 112 cancer 329 1 657 #> 113 normal 332 656 1142 #> 114 cancer 100 433 165 #> 115 normal 131 2076 361 #> 116 normal 622 343 125 #> 117 cancer 203 275 0 #> 118 cancer 256 271 579 #> 119 normal 800 957 1240 #> 120 cancer 910 25 13 #> 121 normal 14 201 34 #> 122 normal 622 392 1 #> 123 cancer 151 45 105 #> 124 normal 678 38 440 #> 125 normal 865 462 62 #> 126 cancer 606 1906 363 #> 127 normal 406 354 628 #> 128 cancer 615 232 89 #> 129 normal 51 195 135 #> 130 cancer 449 435 973 #> 131 cancer 1016 98 15 #> 132 normal 380 320 300 #> 133 cancer 733 216 392 #> 134 cancer 281 549 174 #> 135 cancer 744 8 15 #> 136 normal 377 1019 452 #> 137 cancer 166 850 2336 #> 138 normal 724 224 114 #> 139 cancer 56 282 43 #> 140 normal 765 638 437 #> 141 cancer 55 556 196 #> 142 cancer 30 133 558 #> 143 cancer 50 106 75 #> 144 cancer 116 201 33 #> 145 cancer 237 293 848 #> 146 cancer 193 134 40 #> 147 cancer 401 372 1059 #> 148 cancer 250 167 1338 #> 149 cancer 1434 68 56 #> 150 normal 739 2144 1254 #> 151 cancer 249 2050 751 #> 152 cancer 1311 428 172 #> 153 normal 61 493 303 #> 154 cancer 168 36 71 #> 155 cancer 382 136 60 #> 156 cancer 401 259 169 #> 157 cancer 3540 28 26 #> 158 cancer 757 130 277 #> 159 cancer 1282 69 1331 #> 160 cancer 1401 25 14 #> 161 cancer 189 15 13 #> 162 cancer 627 649 1 #> 163 cancer 468 36 80 #> 164 normal 950 251 211 #> 165 cancer 923 31 58 #> 166 cancer 9 554 557 #> 167 cancer 18 655 496 #> 168 cancer 2671 0 2 #> 169 cancer 2723 17 27 #> 170 cancer 3360 8 5 #> 171 cancer 228 540 205 #> 172 cancer 109 89 35 #> 173 cancer 519 5 7 #> 174 cancer 420 296 131 #> 175 cancer 233 584 261 #> 176 normal 402 299 1365 #> 177 normal 275 231 54 #> 178 cancer 1927 365 218 #> 179 cancer 675 12 10 #> 180 cancer 62 579 96 #> 181 cancer 61 455 168 #> 182 cancer 71 68 242 #> 183 cancer 144 80 6 #> 184 cancer 113 749 128 #> 185 cancer 412 26 4 #> 186 cancer 4 180 234 #> 187 cancer 693 381 59 #> 188 cancer 988 7 4 #> 189 cancer 42 177 289 #> 190 cancer 98 353 146 #> 191 cancer 1139 19 0 #> 192 cancer 1321 4 1 #> 193 normal 852 449 181 #> 194 cancer 446 77 114 #> 195 cancer 266 489 146 #> 196 cancer 1806 10 7 #> 197 cancer 1434 343 1485 #> 198 normal 4170 16 0 #> 199 cancer 1284 198 60 #> 200 cancer 208 598 121
test_df <- mikropml::otu_mini test_df[1:100, "dx"] <- NA rm_missing_outcome(test_df, "dx")
#> Removed 100/200 (50%) of samples because of missing outcome value (NA).
#> dx Otu00001 Otu00002 Otu00003 #> 1 normal 477 289 94 #> 2 cancer 2474 20 12 #> 3 cancer 1216 70 103 #> 4 normal 852 298 470 #> 5 normal 250 873 112 #> 6 normal 475 569 149 #> 7 cancer 129 236 2 #> 8 cancer 388 1079 572 #> 9 cancer 1683 21 38 #> 10 cancer 223 144 63 #> 11 normal 446 1182 520 #> 12 cancer 329 1 657 #> 13 normal 332 656 1142 #> 14 cancer 100 433 165 #> 15 normal 131 2076 361 #> 16 normal 622 343 125 #> 17 cancer 203 275 0 #> 18 cancer 256 271 579 #> 19 normal 800 957 1240 #> 20 cancer 910 25 13 #> 21 normal 14 201 34 #> 22 normal 622 392 1 #> 23 cancer 151 45 105 #> 24 normal 678 38 440 #> 25 normal 865 462 62 #> 26 cancer 606 1906 363 #> 27 normal 406 354 628 #> 28 cancer 615 232 89 #> 29 normal 51 195 135 #> 30 cancer 449 435 973 #> 31 cancer 1016 98 15 #> 32 normal 380 320 300 #> 33 cancer 733 216 392 #> 34 cancer 281 549 174 #> 35 cancer 744 8 15 #> 36 normal 377 1019 452 #> 37 cancer 166 850 2336 #> 38 normal 724 224 114 #> 39 cancer 56 282 43 #> 40 normal 765 638 437 #> 41 cancer 55 556 196 #> 42 cancer 30 133 558 #> 43 cancer 50 106 75 #> 44 cancer 116 201 33 #> 45 cancer 237 293 848 #> 46 cancer 193 134 40 #> 47 cancer 401 372 1059 #> 48 cancer 250 167 1338 #> 49 cancer 1434 68 56 #> 50 normal 739 2144 1254 #> 51 cancer 249 2050 751 #> 52 cancer 1311 428 172 #> 53 normal 61 493 303 #> 54 cancer 168 36 71 #> 55 cancer 382 136 60 #> 56 cancer 401 259 169 #> 57 cancer 3540 28 26 #> 58 cancer 757 130 277 #> 59 cancer 1282 69 1331 #> 60 cancer 1401 25 14 #> 61 cancer 189 15 13 #> 62 cancer 627 649 1 #> 63 cancer 468 36 80 #> 64 normal 950 251 211 #> 65 cancer 923 31 58 #> 66 cancer 9 554 557 #> 67 cancer 18 655 496 #> 68 cancer 2671 0 2 #> 69 cancer 2723 17 27 #> 70 cancer 3360 8 5 #> 71 cancer 228 540 205 #> 72 cancer 109 89 35 #> 73 cancer 519 5 7 #> 74 cancer 420 296 131 #> 75 cancer 233 584 261 #> 76 normal 402 299 1365 #> 77 normal 275 231 54 #> 78 cancer 1927 365 218 #> 79 cancer 675 12 10 #> 80 cancer 62 579 96 #> 81 cancer 61 455 168 #> 82 cancer 71 68 242 #> 83 cancer 144 80 6 #> 84 cancer 113 749 128 #> 85 cancer 412 26 4 #> 86 cancer 4 180 234 #> 87 cancer 693 381 59 #> 88 cancer 988 7 4 #> 89 cancer 42 177 289 #> 90 cancer 98 353 146 #> 91 cancer 1139 19 0 #> 92 cancer 1321 4 1 #> 93 normal 852 449 181 #> 94 cancer 446 77 114 #> 95 cancer 266 489 146 #> 96 cancer 1806 10 7 #> 97 cancer 1434 343 1485 #> 98 normal 4170 16 0 #> 99 cancer 1284 198 60 #> 100 cancer 208 598 121