Extracts feature importance in random forest in a nice format.
Examples
data(example_set)
rf <- fit_rf(example_set, y = "Group")
rf
#>
#> Call:
#> randomForest(x = x, y = colData(object)[, y], importance = importance)
#> Type of random forest: classification
#> Number of trees: 500
#> No. of variables tried at each split: 8
#>
#> OOB estimate of error rate: 48%
#> Confusion matrix:
#> A B QC class.error
#> A 15 5 0 0.25
#> B 11 9 0 0.55
#> QC 4 4 2 0.80
importance_rf(rf)
#> Feature_ID A B
#> HILIC_neg_259_9623a4_4322 HILIC_neg_259_9623a4_4322 1.616667e-03 -1.952381e-03
#> HILIC_neg_108_1065a2_6121 HILIC_neg_108_1065a2_6121 -1.095960e-03 2.987302e-03
#> HILIC_neg_158_23a1_4128 HILIC_neg_158_23a1_4128 -3.826118e-03 1.934055e-03
#> HILIC_neg_251_0056a0_6161 HILIC_neg_251_0056a0_6161 3.142857e-04 -2.682540e-04
#> HILIC_neg_401_52a4_211 HILIC_neg_401_52a4_211 -3.445166e-04 -3.000000e-04
#> HILIC_neg_400_7045a5_3842 HILIC_neg_400_7045a5_3842 3.246032e-04 3.204040e-03
#> HILIC_neg_304_014a7_1311 HILIC_neg_304_014a7_1311 1.292807e-03 1.651515e-04
#> HILIC_neg_276_6328a2_7734 HILIC_neg_276_6328a2_7734 1.235714e-03 1.523810e-04
#> HILIC_neg_118_9111a4_1865 HILIC_neg_118_9111a4_1865 3.594517e-04 1.521429e-03
#> HILIC_neg_446_9413a2_315 HILIC_neg_446_9413a2_315 -9.675325e-04 2.678644e-03
#> HILIC_neg_127_5856a4_3758 HILIC_neg_127_5856a4_3758 -1.681818e-04 1.688961e-03
#> HILIC_neg_303_2144a1_2372 HILIC_neg_303_2144a1_2372 4.461039e-04 9.793651e-04
#> HILIC_neg_366_6203a6_1825 HILIC_neg_366_6203a6_1825 6.063492e-04 4.268398e-04
#> HILIC_neg_258_7252a7_5445 HILIC_neg_258_7252a7_5445 -3.450000e-03 -1.161905e-03
#> HILIC_neg_301_2643a4_0372 HILIC_neg_301_2643a4_0372 1.752525e-03 1.177128e-03
#> HILIC_neg_224_4031a4_7409 HILIC_neg_224_4031a4_7409 -2.040404e-03 1.569841e-03
#> HILIC_neg_424_8488a6_7736 HILIC_neg_424_8488a6_7736 3.707937e-03 5.683261e-04
#> HILIC_neg_131_2034a6_1385 HILIC_neg_131_2034a6_1385 -3.531025e-04 2.722944e-03
#> HILIC_neg_236_4114a5_6302 HILIC_neg_236_4114a5_6302 -1.349278e-03 -2.551515e-03
#> HILIC_neg_411_0148a0_7484 HILIC_neg_411_0148a0_7484 2.791708e-04 -2.121573e-03
#> HILIC_pos_288_6263a6_572 HILIC_pos_288_6263a6_572 -3.315873e-03 1.753968e-04
#> HILIC_pos_331_1173a7_7822 HILIC_pos_331_1173a7_7822 -2.601732e-03 -2.928571e-04
#> HILIC_pos_139_4044a6_0388 HILIC_pos_139_4044a6_0388 -1.925469e-03 -1.138095e-03
#> HILIC_pos_132_7373a6_4146 HILIC_pos_132_7373a6_4146 1.623160e-03 2.500000e-03
#> HILIC_pos_298_6144a3_839 HILIC_pos_298_6144a3_839 -7.430014e-04 -3.011905e-03
#> HILIC_pos_410_9203a2_7329 HILIC_pos_410_9203a2_7329 9.014214e-03 -1.845310e-03
#> HILIC_pos_145_8514a2_811 HILIC_pos_145_8514a2_811 -8.293651e-04 -2.461111e-03
#> HILIC_pos_306_0061a4_4049 HILIC_pos_306_0061a4_4049 1.262121e-03 -1.461111e-03
#> HILIC_pos_425_8858a4_4494 HILIC_pos_425_8858a4_4494 2.680231e-03 2.777778e-05
#> HILIC_pos_436_332a6_1165 HILIC_pos_436_332a6_1165 -1.697691e-03 -2.208802e-03
#> HILIC_pos_255_0094a7_9288 HILIC_pos_255_0094a7_9288 -7.277778e-04 -4.357143e-04
#> HILIC_pos_417_1474a2_8239 HILIC_pos_417_1474a2_8239 -2.112698e-03 -5.182540e-04
#> HILIC_pos_297_8334a0_6647 HILIC_pos_297_8334a0_6647 5.769841e-04 -9.373737e-04
#> HILIC_pos_449_2162a0_7574 HILIC_pos_449_2162a0_7574 2.483405e-04 5.921356e-04
#> HILIC_pos_197_7438a7_72 HILIC_pos_197_7438a7_72 -3.552453e-03 2.022222e-03
#> HILIC_pos_141_601a7_387 HILIC_pos_141_601a7_387 1.992063e-04 -5.992063e-04
#> HILIC_pos_448_1172a6_8567 HILIC_pos_448_1172a6_8567 -3.372222e-03 -5.166667e-04
#> HILIC_pos_346_6405a3_2719 HILIC_pos_346_6405a3_2719 -2.885714e-03 3.460317e-04
#> HILIC_pos_334_3285a1_7395 HILIC_pos_334_3285a1_7395 -1.381674e-04 2.269120e-04
#> HILIC_pos_215_5364a2_6707 HILIC_pos_215_5364a2_6707 -1.213492e-03 -2.166883e-03
#> RP_neg_458_0877a1_5798 RP_neg_458_0877a1_5798 1.491342e-03 3.584848e-03
#> RP_neg_365_8511a5_6086 RP_neg_365_8511a5_6086 -5.571429e-04 -2.371429e-03
#> RP_neg_369_5116a6_4389 RP_neg_369_5116a6_4389 4.165079e-03 -1.814358e-03
#> RP_neg_222_4828a6_0392 RP_neg_222_4828a6_0392 4.320635e-03 1.375483e-02
#> RP_neg_114_84a3_0917 RP_neg_114_84a3_0917 1.648413e-03 -1.560317e-03
#> RP_neg_317_554a3_063 RP_neg_317_554a3_063 4.815079e-03 6.144444e-03
#> RP_neg_419_897a3_9617 RP_neg_419_897a3_9617 2.717838e-05 -2.196970e-03
#> RP_neg_493_3039a6_7816 RP_neg_493_3039a6_7816 1.826118e-04 -1.701587e-03
#> RP_neg_359_0517a7_3652 RP_neg_359_0517a7_3652 -1.224359e-03 1.666667e-04
#> RP_neg_435_8009a6_2215 RP_neg_435_8009a6_2215 8.261183e-05 -4.342136e-03
#> RP_neg_358_2061a5_2818 RP_neg_358_2061a5_2818 1.873665e-03 -9.507937e-04
#> RP_neg_397_2502a3_7998 RP_neg_397_2502a3_7998 1.007937e-03 -6.286436e-04
#> RP_neg_165_9294a3_4261 RP_neg_165_9294a3_4261 -7.380952e-04 -7.896825e-04
#> RP_neg_413_1764a3_6741 RP_neg_413_1764a3_6741 8.151515e-04 3.252525e-04
#> RP_neg_115_4062a7_7329 RP_neg_115_4062a7_7329 -6.618326e-04 -1.166667e-04
#> RP_neg_300_1295a1_6959 RP_neg_300_1295a1_6959 1.230159e-03 3.539683e-04
#> RP_neg_177_6084a5_2913 RP_neg_177_6084a5_2913 -1.810317e-03 -6.142857e-04
#> RP_neg_134_1196a2_9606 RP_neg_134_1196a2_9606 -3.888889e-05 6.579365e-04
#> RP_neg_139_4456a4_1251 RP_neg_139_4456a4_1251 4.612648e-03 5.306349e-03
#> RP_neg_385_6867a4_136 RP_neg_385_6867a4_136 -1.262698e-03 1.007937e-04
#> RP_pos_490_9235a4_0176 RP_pos_490_9235a4_0176 1.533333e-03 1.175469e-03
#> RP_pos_383_4976a2_6503 RP_pos_383_4976a2_6503 2.316861e-03 -2.817460e-04
#> RP_pos_344_9911a1_9656 RP_pos_344_9911a1_9656 -4.540404e-04 1.215007e-03
#> RP_pos_117_7095a4_0945 RP_pos_117_7095a4_0945 -6.111111e-04 2.380952e-06
#> RP_pos_294_9596a6_7569 RP_pos_294_9596a6_7569 -1.398341e-03 3.809524e-04
#> RP_pos_460_4815a0_8843 RP_pos_460_4815a0_8843 7.904473e-03 -3.280231e-03
#> RP_pos_272_3545a3_5592 RP_pos_272_3545a3_5592 -6.634921e-04 -4.690476e-04
#> RP_pos_409_2445a2_4149 RP_pos_409_2445a2_4149 -1.123016e-03 -7.539683e-05
#> RP_pos_245_9925a3_6251 RP_pos_245_9925a3_6251 -5.468975e-05 1.611111e-04
#> RP_pos_369_1069a1_6271 RP_pos_369_1069a1_6271 -2.738817e-04 -2.940476e-03
#> RP_pos_174_0715a4_3465 RP_pos_174_0715a4_3465 5.732323e-04 3.179509e-03
#> RP_pos_324_6195a4_7743 RP_pos_324_6195a4_7743 2.300938e-03 -6.522367e-05
#> RP_pos_149_432a4_1341 RP_pos_149_432a4_1341 -2.421429e-03 -2.460317e-05
#> RP_pos_461_5891a7_1505 RP_pos_461_5891a7_1505 7.050794e-03 1.434005e-03
#> RP_pos_458_263a4_3477 RP_pos_458_263a4_3477 5.612554e-04 -3.555556e-04
#> RP_pos_226_7218a3_1371 RP_pos_226_7218a3_1371 -2.879437e-03 8.809524e-04
#> RP_pos_280_3779a4_0424 RP_pos_280_3779a4_0424 -1.443001e-06 5.029582e-04
#> RP_pos_447_3232a2_2393 RP_pos_447_3232a2_2393 -1.950866e-03 -8.540404e-04
#> RP_pos_453_282a5_128 RP_pos_453_282a5_128 -4.476190e-04 1.173810e-03
#> RP_pos_153_9636a7_9986 RP_pos_153_9636a7_9986 1.970829e-03 1.796032e-03
#> QC MeanDecreaseAccuracy MeanDecreaseGini
#> HILIC_neg_259_9623a4_4322 2.400000e-03 3.066175e-04 0.3528518
#> HILIC_neg_108_1065a2_6121 3.566667e-03 1.014352e-03 0.3138330
#> HILIC_neg_158_23a1_4128 3.166667e-03 -4.369480e-04 0.3280608
#> HILIC_neg_251_0056a0_6161 -2.600000e-03 -4.589124e-05 0.3752928
#> HILIC_neg_401_52a4_211 3.366667e-03 4.070062e-04 0.4361627
#> HILIC_neg_400_7045a5_3842 9.100000e-03 2.621228e-03 0.6078230
#> HILIC_neg_304_014a7_1311 -1.500000e-03 5.133867e-04 0.3039561
#> HILIC_neg_276_6328a2_7734 -7.666667e-04 4.405938e-04 0.2250095
#> HILIC_neg_118_9111a4_1865 3.000000e-04 7.096941e-04 0.3984765
#> HILIC_neg_446_9413a2_315 -6.666667e-04 5.241457e-05 0.1681697
#> HILIC_neg_127_5856a4_3758 -2.333333e-03 -5.396273e-05 0.3212593
#> HILIC_neg_303_2144a1_2372 2.433333e-03 6.774455e-04 0.3221395
#> HILIC_neg_366_6203a6_1825 1.866667e-03 1.017298e-03 0.3566595
#> HILIC_neg_258_7252a7_5445 9.000000e-04 -1.073779e-03 0.5214690
#> HILIC_neg_301_2643a4_0372 -1.733333e-03 1.045124e-03 0.2986726
#> HILIC_neg_224_4031a4_7409 3.866667e-03 8.964195e-04 0.3213630
#> HILIC_neg_424_8488a6_7736 8.733333e-03 3.717326e-03 0.6571522
#> HILIC_neg_131_2034a6_1385 3.666667e-03 1.475920e-03 0.3041777
#> HILIC_neg_236_4114a5_6302 -2.171429e-03 -1.589113e-03 0.4244208
#> HILIC_neg_411_0148a0_7484 3.571429e-03 3.548476e-04 0.4441159
#> HILIC_pos_288_6263a6_572 1.150000e-03 -8.289494e-04 0.2202516
#> HILIC_pos_331_1173a7_7822 6.585714e-03 2.088111e-04 0.3177510
#> HILIC_pos_139_4044a6_0388 -1.666667e-03 -1.506580e-03 0.3613624
#> HILIC_pos_132_7373a6_4146 3.185714e-03 2.496701e-03 0.5345994
#> HILIC_pos_298_6144a3_839 2.733333e-03 -6.652521e-04 0.3183029
#> HILIC_pos_410_9203a2_7329 1.086667e-02 4.723847e-03 0.7728827
#> HILIC_pos_145_8514a2_811 -6.666667e-04 -1.702240e-03 0.2716367
#> HILIC_pos_306_0061a4_4049 3.000000e-03 1.964515e-04 0.3678906
#> HILIC_pos_425_8858a4_4494 -2.466667e-03 5.413264e-04 0.2730234
#> HILIC_pos_436_332a6_1165 1.200000e-03 -9.797226e-04 0.2361371
#> HILIC_pos_255_0094a7_9288 1.266667e-03 -2.511094e-04 0.2384000
#> HILIC_pos_417_1474a2_8239 2.052381e-03 -4.019299e-04 0.4486455
#> HILIC_pos_297_8334a0_6647 -1.110223e-19 -1.896971e-04 0.2458268
#> HILIC_pos_449_2162a0_7574 1.568571e-02 3.038663e-03 0.6008917
#> HILIC_pos_197_7438a7_72 1.015238e-02 1.041810e-03 0.4806152
#> HILIC_pos_141_601a7_387 -3.855556e-03 -9.039216e-04 0.3180582
#> HILIC_pos_448_1172a6_8567 5.700000e-03 -2.496850e-05 0.2822332
#> HILIC_pos_346_6405a3_2719 2.466667e-03 -2.313992e-04 0.3162277
#> HILIC_pos_334_3285a1_7395 4.400000e-03 9.142713e-04 0.3901337
#> HILIC_pos_215_5364a2_6707 5.000000e-04 -1.281154e-03 0.2416363
#> RP_neg_458_0877a1_5798 2.000000e-04 1.890429e-03 0.5428883
#> RP_neg_365_8511a5_6086 3.000000e-03 -8.513760e-04 0.2099833
#> RP_neg_369_5116a6_4389 5.661905e-03 1.690248e-03 0.8317551
#> RP_neg_222_4828a6_0392 3.500000e-03 7.276089e-03 0.9085766
#> RP_neg_114_84a3_0917 4.166667e-03 9.867154e-04 0.7800590
#> RP_neg_317_554a3_063 3.719048e-03 4.604729e-03 0.6987228
#> RP_neg_419_897a3_9617 3.333333e-03 -2.659171e-04 0.3555057
#> RP_neg_493_3039a6_7816 -1.052381e-03 -7.335251e-04 0.2416877
#> RP_neg_359_0517a7_3652 2.000000e-03 -1.577290e-04 0.1645055
#> RP_neg_435_8009a6_2215 6.433333e-03 -8.801949e-04 0.5645848
#> RP_neg_358_2061a5_2818 -2.966667e-03 -6.382409e-04 0.4081995
#> RP_neg_397_2502a3_7998 1.266667e-03 3.215089e-04 0.2268712
#> RP_neg_165_9294a3_4261 1.466667e-03 -6.093472e-04 0.2713563
#> RP_neg_413_1764a3_6741 -1.000000e-03 1.524272e-04 0.2940782
#> RP_neg_115_4062a7_7329 5.133333e-03 7.509362e-04 0.4084590
#> RP_neg_300_1295a1_6959 -1.100000e-03 4.299941e-04 0.3403362
#> RP_neg_177_6084a5_2913 7.352381e-03 4.134515e-04 0.3118073
#> RP_neg_134_1196a2_9606 -1.600000e-03 -8.856086e-05 0.2135450
#> RP_neg_139_4456a4_1251 -6.666667e-04 3.173709e-03 0.6838947
#> RP_neg_385_6867a4_136 2.666667e-03 -1.946071e-04 0.2544628
#> RP_pos_490_9235a4_0176 4.052381e-03 1.625588e-03 0.2697409
#> RP_pos_383_4976a2_6503 1.333333e-04 1.039508e-03 0.5210794
#> RP_pos_344_9911a1_9656 3.766667e-03 7.567239e-04 0.2630070
#> RP_pos_117_7095a4_0945 9.190476e-04 3.298532e-05 0.1546072
#> RP_pos_294_9596a6_7569 1.233333e-03 -8.966422e-05 0.2665878
#> RP_pos_460_4815a0_8843 1.820476e-02 4.886752e-03 0.8931058
#> RP_pos_272_3545a3_5592 2.333333e-04 -3.658850e-04 0.2662781
#> RP_pos_409_2445a2_4149 3.900000e-03 -1.443850e-04 0.2244028
#> RP_pos_245_9925a3_6251 -8.476190e-04 -2.902390e-04 0.3300598
#> RP_pos_369_1069a1_6271 6.400000e-03 -3.477783e-04 0.3066665
#> RP_pos_174_0715a4_3465 2.733333e-03 2.332519e-03 0.2807195
#> RP_pos_324_6195a4_7743 -3.433333e-03 3.874968e-04 0.3519453
#> RP_pos_149_432a4_1341 4.666667e-04 -9.720988e-04 0.3715794
#> RP_pos_461_5891a7_1505 1.223810e-02 5.657739e-03 0.7578792
#> RP_pos_458_263a4_3477 5.633333e-03 1.040435e-03 0.3869341
#> RP_pos_226_7218a3_1371 4.166667e-03 7.289596e-04 0.3255116
#> RP_pos_280_3779a4_0424 6.400000e-03 1.218840e-03 0.5905074
#> RP_pos_447_3232a2_2393 2.666667e-03 -9.974242e-04 0.3440355
#> RP_pos_453_282a5_128 -2.933333e-03 -3.675164e-05 0.3835782
#> RP_pos_153_9636a7_9986 2.566667e-03 1.566978e-03 0.5862039