Feature selection using Boruta
Examples
library(dplyr)
#>
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#>
#> filter, lag
#> The following objects are masked from ‘package:base’:
#>
#> intersect, setdiff, setequal, union
meta_dat1 <- t(meta_dat) %>%
as.data.frame() %>%
dplyr::mutate(group=group)
result_ML_Boruta <- ML_Boruta(meta_dat1)
#> 1. run of importance source...
#> 2. run of importance source...
#> 3. run of importance source...
#> 4. run of importance source...
#> 5. run of importance source...
#> 6. run of importance source...
#> 7. run of importance source...
#> 8. run of importance source...
#> 9. run of importance source...
#> 10. run of importance source...
#> 11. run of importance source...
#> 12. run of importance source...
#> 13. run of importance source...
#> 14. run of importance source...
#> 15. run of importance source...
#> After 15 iterations, +0.59 secs:
#> confirmed 20 attributes: C00022, C00025, C00042, C00073, C00148 and 15 more;
#> rejected 121 attributes: C00002, C00003, C00006, C00008, C00015 and 116 more;
#> still have 78 attributes left.
#> 16. run of importance source...
#> 17. run of importance source...
#> 18. run of importance source...
#> 19. run of importance source...
#> After 19 iterations, +0.69 secs:
#> rejected 13 attributes: C00016, C00020, C00021, C00035, C00055 and 8 more;
#> still have 65 attributes left.
#> 20. run of importance source...
#> 21. run of importance source...
#> 22. run of importance source...
#> 23. run of importance source...
#> After 23 iterations, +0.77 secs:
#> confirmed 1 attribute: C00490;
#> rejected 5 attributes: C00043, C00078, C00093, C02862, C05401;
#> still have 59 attributes left.
#> 24. run of importance source...
#> 25. run of importance source...
#> 26. run of importance source...
#> After 26 iterations, +0.84 secs:
#> confirmed 4 attributes: C00079, C00153, C00570, C05673;
#> rejected 3 attributes: C00152, C00188, C03740;
#> still have 52 attributes left.
#> 27. run of importance source...
#> 28. run of importance source...
#> 29. run of importance source...
#> 30. run of importance source...
#> After 30 iterations, +0.92 secs:
#> confirmed 1 attribute: C00167;
#> rejected 2 attributes: C00004, C00791;
#> still have 49 attributes left.
#> 31. run of importance source...
#> 32. run of importance source...
#> 33. run of importance source...
#> After 33 iterations, +0.98 secs:
#> confirmed 3 attributes: C00149, C00170, C00447;
#> rejected 2 attributes: C00183, C00800;
#> still have 44 attributes left.
#> 34. run of importance source...
#> 35. run of importance source...
#> 36. run of importance source...
#> After 36 iterations, +1 secs:
#> confirmed 2 attributes: C00307, C03406;
#> rejected 2 attributes: C00064, C11924;
#> still have 40 attributes left.
#> 37. run of importance source...
#> 38. run of importance source...
#> 39. run of importance source...
#> 40. run of importance source...
#> 41. run of importance source...
#> 42. run of importance source...
#> 43. run of importance source...
#> 44. run of importance source...
#> 45. run of importance source...
#> 46. run of importance source...
#> 47. run of importance source...
#> 48. run of importance source...
#> After 48 iterations, +1.3 secs:
#> rejected 2 attributes: C00158, C00624;
#> still have 38 attributes left.
#> 49. run of importance source...
#> 50. run of importance source...
#> After 50 iterations, +1.3 secs:
#> rejected 2 attributes: C00385, C00438;
#> still have 36 attributes left.
#> 51. run of importance source...
#> 52. run of importance source...
#> 53. run of importance source...
#> 54. run of importance source...
#> 55. run of importance source...
#> 56. run of importance source...
#> After 56 iterations, +1.5 secs:
#> rejected 1 attribute: C05100;
#> still have 35 attributes left.
#> 57. run of importance source...
#> 58. run of importance source...
#> 59. run of importance source...
#> After 59 iterations, +1.5 secs:
#> confirmed 2 attributes: C00013, C00097;
#> still have 33 attributes left.
#> 60. run of importance source...
#> 61. run of importance source...
#> After 61 iterations, +1.6 secs:
#> confirmed 1 attribute: C00352;
#> rejected 1 attribute: C01419;
#> still have 31 attributes left.
#> 62. run of importance source...
#> 63. run of importance source...
#> 64. run of importance source...
#> 65. run of importance source...
#> 66. run of importance source...
#> 67. run of importance source...
#> 68. run of importance source...
#> 69. run of importance source...
#> After 69 iterations, +1.7 secs:
#> confirmed 2 attributes: C00010, C06192;
#> still have 29 attributes left.
#> 70. run of importance source...
#> 71. run of importance source...
#> 72. run of importance source...
#> After 72 iterations, +1.8 secs:
#> rejected 1 attribute: C00037;
#> still have 28 attributes left.
#> 73. run of importance source...
#> 74. run of importance source...
#> 75. run of importance source...
#> After 75 iterations, +1.8 secs:
#> rejected 1 attribute: C00408;
#> still have 27 attributes left.
#> 76. run of importance source...
#> 77. run of importance source...
#> 78. run of importance source...
#> 79. run of importance source...
#> 80. run of importance source...
#> After 80 iterations, +1.9 secs:
#> rejected 1 attribute: C16513;
#> still have 26 attributes left.
#> 81. run of importance source...
#> 82. run of importance source...
#> 83. run of importance source...
#> 84. run of importance source...
#> 85. run of importance source...
#> 86. run of importance source...
#> 87. run of importance source...
#> 88. run of importance source...
#> 89. run of importance source...
#> 90. run of importance source...
#> 91. run of importance source...
#> 92. run of importance source...
#> 93. run of importance source...
#> 94. run of importance source...
#> 95. run of importance source...
#> 96. run of importance source...
#> 97. run of importance source...
#> 98. run of importance source...
#> 99. run of importance source...
#> 100. run of importance source...
#> 101. run of importance source...
#> 102. run of importance source...
#> 103. run of importance source...
#> 104. run of importance source...
#> 105. run of importance source...
#> 106. run of importance source...
#> 107. run of importance source...
#> 108. run of importance source...
#> 109. run of importance source...
#> 110. run of importance source...
#> 111. run of importance source...
#> 112. run of importance source...
#> 113. run of importance source...
#> 114. run of importance source...
#> 115. run of importance source...
#> 116. run of importance source...
#> 117. run of importance source...
#> After 117 iterations, +2.7 secs:
#> confirmed 1 attribute: C00106;
#> still have 25 attributes left.
#> 118. run of importance source...
#> 119. run of importance source...
#> 120. run of importance source...
#> 121. run of importance source...
#> 122. run of importance source...
#> 123. run of importance source...
#> 124. run of importance source...
#> 125. run of importance source...
#> 126. run of importance source...
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#> 128. run of importance source...
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#> 130. run of importance source...
#> 131. run of importance source...
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#> 133. run of importance source...
#> 134. run of importance source...
#> 135. run of importance source...
#> 136. run of importance source...
#> 137. run of importance source...
#> 138. run of importance source...
#> 139. run of importance source...
#> 140. run of importance source...
#> 141. run of importance source...
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#> 143. run of importance source...
#> 144. run of importance source...
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#> 157. run of importance source...
#> 158. run of importance source...
#> 159. run of importance source...
#> 160. run of importance source...
#> 161. run of importance source...
#> After 161 iterations, +3.5 secs:
#> confirmed 1 attribute: C00670;
#> still have 24 attributes left.
#> 162. run of importance source...
#> 163. run of importance source...
#> 164. run of importance source...
#> 165. run of importance source...
#> 166. run of importance source...
#> 167. run of importance source...
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#> 220. run of importance source...
#> 221. run of importance source...
#> 222. run of importance source...
#> 223. run of importance source...
#> 224. run of importance source...
#> 225. run of importance source...
#> 226. run of importance source...
#> 227. run of importance source...
#> 228. run of importance source...
#> 229. run of importance source...
#> 230. run of importance source...
#> 231. run of importance source...
#> 232. run of importance source...
#> 233. run of importance source...
#> 234. run of importance source...
#> 235. run of importance source...
#> 236. run of importance source...
#> 237. run of importance source...
#> 238. run of importance source...
#> 239. run of importance source...
#> 240. run of importance source...
#> 241. run of importance source...
#> 242. run of importance source...
#> 243. run of importance source...
#> 244. run of importance source...
#> 245. run of importance source...
#> 246. run of importance source...
#> 247. run of importance source...
#> 248. run of importance source...
#> 249. run of importance source...
#> 250. run of importance source...
#> 251. run of importance source...
#> After 251 iterations, +5.2 secs:
#> rejected 1 attribute: C00065;
#> still have 23 attributes left.
#> 252. run of importance source...
#> 253. run of importance source...
#> 254. run of importance source...
#> 255. run of importance source...
#> 256. run of importance source...
#> 257. run of importance source...
#> 258. run of importance source...
#> 259. run of importance source...
#> 260. run of importance source...
#> 261. run of importance source...
#> 262. run of importance source...
#> 263. run of importance source...
#> 264. run of importance source...
#> 265. run of importance source...
#> 266. run of importance source...
#> 267. run of importance source...
#> 268. run of importance source...
#> 269. run of importance source...
#> 270. run of importance source...
#> 271. run of importance source...
#> 272. run of importance source...
#> 273. run of importance source...
#> 274. run of importance source...
#> 275. run of importance source...
#> 276. run of importance source...
#> 277. run of importance source...
#> 278. run of importance source...
#> 279. run of importance source...
#> 280. run of importance source...
#> 281. run of importance source...
#> 282. run of importance source...
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#> 284. run of importance source...
#> 285. run of importance source...
#> 286. run of importance source...
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#> 288. run of importance source...
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#> 290. run of importance source...
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#> 292. run of importance source...
#> 293. run of importance source...
#> 294. run of importance source...
#> 295. run of importance source...
#> 296. run of importance source...
#> 297. run of importance source...
#> 298. run of importance source...
#> 299. run of importance source...
#> 300. run of importance source...
#> 301. run of importance source...
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#> 312. run of importance source...
#> 313. run of importance source...
#> 314. run of importance source...
#> 315. run of importance source...
#> 316. run of importance source...
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#> 340. run of importance source...
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#> 343. run of importance source...
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#> 345. run of importance source...
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#> 350. run of importance source...
#> 351. run of importance source...
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#> 354. run of importance source...
#> 355. run of importance source...
#> 356. run of importance source...
#> 357. run of importance source...
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#> 359. run of importance source...
#> 360. run of importance source...
#> 361. run of importance source...
#> 362. run of importance source...
#> 363. run of importance source...
#> 364. run of importance source...
#> 365. run of importance source...
#> 366. run of importance source...
#> 367. run of importance source...
#> 368. run of importance source...
#> 369. run of importance source...
#> 370. run of importance source...
#> 371. run of importance source...
#> 372. run of importance source...
#> 373. run of importance source...
#> 374. run of importance source...
#> 375. run of importance source...
#> 376. run of importance source...
#> 377. run of importance source...
#> 378. run of importance source...
#> 379. run of importance source...
#> 380. run of importance source...
#> 381. run of importance source...
#> 382. run of importance source...
#> 383. run of importance source...
#> 384. run of importance source...
#> After 384 iterations, +7.7 secs:
#> rejected 1 attribute: C00186;
#> still have 22 attributes left.
#> 385. run of importance source...
#> 386. run of importance source...
#> 387. run of importance source...
#> 388. run of importance source...
#> After 388 iterations, +7.8 secs:
#> confirmed 1 attribute: C13482;
#> still have 21 attributes left.
#> 389. run of importance source...
#> 390. run of importance source...
#> 391. run of importance source...
#> 392. run of importance source...
#> 393. run of importance source...
#> 394. run of importance source...
#> 395. run of importance source...
#> 396. run of importance source...
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#> 399. run of importance source...
#> 400. run of importance source...
#> 401. run of importance source...
#> 402. run of importance source...
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#> 404. run of importance source...
#> 405. run of importance source...
#> 406. run of importance source...
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#> 409. run of importance source...
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#> 411. run of importance source...
#> 412. run of importance source...
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#> 415. run of importance source...
#> 416. run of importance source...
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#> 419. run of importance source...
#> 420. run of importance source...
#> 421. run of importance source...
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#> 424. run of importance source...
#> 425. run of importance source...
#> 426. run of importance source...
#> 427. run of importance source...
#> 428. run of importance source...
#> 429. run of importance source...
#> 430. run of importance source...
#> 431. run of importance source...
#> 432. run of importance source...
#> 433. run of importance source...
#> 434. run of importance source...
#> 435. run of importance source...
#> 436. run of importance source...
#> 437. run of importance source...
#> 438. run of importance source...
#> 439. run of importance source...
#> 440. run of importance source...
#> 441. run of importance source...
#> After 441 iterations, +8.8 secs:
#> confirmed 1 attribute: C03264;
#> still have 20 attributes left.
#> 442. run of importance source...
#> 443. run of importance source...
#> 444. run of importance source...
#> 445. run of importance source...
#> 446. run of importance source...
#> 447. run of importance source...
#> 448. run of importance source...
#> 449. run of importance source...
#> 450. run of importance source...
#> 451. run of importance source...
#> 452. run of importance source...
#> 453. run of importance source...
#> 454. run of importance source...
#> 455. run of importance source...
#> 456. run of importance source...
#> 457. run of importance source...
#> 458. run of importance source...
#> 459. run of importance source...
#> After 459 iterations, +9.2 secs:
#> confirmed 1 attribute: C00601;
#> still have 19 attributes left.
#> 460. run of importance source...
#> 461. run of importance source...
#> 462. run of importance source...
#> 463. run of importance source...
#> 464. run of importance source...
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#> 494. run of importance source...
#> 495. run of importance source...
#> 496. run of importance source...
#> 497. run of importance source...
#> 498. run of importance source...
#> 499. run of importance source...
result_ML_Boruta
#> name meanImp medianImp minImp maxImp normHits decision
#> 1 C03264 1.807909 1.890535 -1.00100150 3.192239 0.6052104 Confirmed
#> 2 C02630 3.903959 3.907530 2.23148770 5.273588 1.0000000 Confirmed
#> 3 C00170 2.320263 2.384736 0.03629764 3.677534 0.8496994 Confirmed
#> 4 C18170 3.504635 3.485503 1.99657024 4.950293 0.9979960 Confirmed
#> 5 C06192 2.226020 2.252420 -0.15535207 3.605125 0.8136273 Confirmed
#> 6 C00267 4.249565 4.265181 2.71962194 5.732876 1.0000000 Confirmed
#> 7 C05378 3.372549 3.400252 1.00100150 4.580840 0.9979960 Confirmed
#> 8 C00307 2.431422 2.465864 0.38834251 3.890010 0.8677355 Confirmed
#> 9 C00570 2.377709 2.425383 0.67975787 4.025020 0.8737475 Confirmed
#> 10 C05673 2.059550 2.120350 -1.00100150 3.575686 0.7114228 Confirmed
#> 11 C05674 4.205880 4.245613 2.58794798 5.596388 1.0000000 Confirmed
#> 12 C00010 2.174915 2.176662 -0.54707777 3.729528 0.7735471 Confirmed
#> 13 C00352 1.960835 1.993343 0.40702693 3.375289 0.6873747 Confirmed
#> 14 C00013 2.418982 2.458271 -0.06025382 3.989990 0.8597194 Confirmed
#> 15 C00365 3.986083 3.989186 2.65324954 5.022842 1.0000000 Confirmed
#> 16 C00242 3.865878 3.867330 1.64777354 5.141176 1.0000000 Confirmed
#> 17 C00490 2.567883 2.609922 0.88561200 3.729620 0.9238477 Confirmed
#> 18 C05938 3.784330 3.779723 1.97520352 5.319923 0.9959920 Confirmed
#> 19 C02291 4.342143 4.343853 2.51348249 6.195052 1.0000000 Confirmed
#> 20 C00097 2.104833 2.160514 -0.44730307 3.626908 0.7595190 Confirmed
#> 21 C02045 5.110886 5.131432 2.60233105 6.487123 1.0000000 Confirmed
#> 22 C02985 3.737106 3.755093 2.15106877 5.022963 1.0000000 Confirmed
#> 23 C00025 3.821855 3.828091 2.04405647 5.132712 1.0000000 Confirmed
#> 24 C00407 3.495083 3.506900 2.00369990 4.711387 0.9959920 Confirmed
#> 25 C00073 5.108951 5.155963 2.74064717 6.408177 1.0000000 Confirmed
#> 26 C00079 2.437029 2.460363 0.84391892 3.742544 0.8937876 Confirmed
#> 27 C00148 3.453752 3.478979 2.00903725 4.781362 0.9959920 Confirmed
#> 28 C00149 2.836733 2.851271 0.62012980 4.104433 0.9519038 Confirmed
#> 29 C03406 2.351666 2.409619 -0.42844806 3.709005 0.8517034 Confirmed
#> 30 C03413 3.628541 3.635069 2.11701431 5.051383 1.0000000 Confirmed
#> 31 C03793 2.488445 2.520756 -0.20814671 3.811534 0.8957916 Confirmed
#> 32 C00153 2.415627 2.463387 0.06726758 3.640149 0.8717435 Confirmed
#> 33 C00601 1.793065 1.851176 -0.39858311 3.323290 0.5911824 Confirmed
#> 34 C13482 1.815757 1.883224 -1.61006779 3.097376 0.6112224 Confirmed
#> 35 C00022 4.245764 4.271655 2.81372115 5.689834 1.0000000 Confirmed
#> 36 C00255 3.766215 3.775998 2.42772492 5.136435 1.0000000 Confirmed
#> 37 C00447 2.364507 2.376125 -0.79140096 3.842949 0.8717435 Confirmed
#> 38 C00670 1.913253 1.923820 -1.00100150 3.101893 0.6613226 Confirmed
#> 39 C00042 3.502316 3.514991 1.95045560 4.721383 1.0000000 Confirmed
#> 40 C00167 2.357317 2.370685 -0.19598929 3.843674 0.8577154 Confirmed
#> 41 C00106 1.847891 1.908517 -0.84142528 3.113480 0.6352705 Confirmed