Run all models. Trains and tests Decision Tree, Random Forest and SVM models on 100 subsamples and provides a summary of the results, to select the best model. The number of trees and kernel chosen by select_svm_kernel and select_rf_numtrees should be used for SVM and Random Forest respectively. We can use this function to inform feature selection, using a Decision Tree voting scheme and a Random Forest measure based on the Gini index.

runallmodels(
  num_trees = 20,
  kernel = "linear",
  degree = 3,
  poly = 0,
  file_path = file_path,
  num_runs = 100
)

Arguments

num_trees	Number of trees for random forest (selected using select_rf_numtrees)
kernel	Kernel for SVM (select using select_svm_kernel)
degree	Degree for SVM kernel (not necessary for linear or sigmoid functions)
poly	1 if polynomial kernel is used, 0 if linear, radial or sigmoid.
file_path	Where the <=num_runs subsample files are found (e.g. if sample 10 is at 'subsamples/sample10.csv' then file_path should be 'subsamples/sample')
num_runs	Number of subsamples to loop over (default: 100)

Value

The function will output a data.frame of the achieved test and training accuracy, sensitivity and specificity for each model on each subsample. Summary boxplots showing accuracy, sensitivity and specificity for each model will be produced. The function will also output dtreevote containing the features used in the decision trees for each subsample and the level of the tree at which they appear. Finally, the function outputs ongoingginis which contains the Gini index for each feature in the Random Forest for each subsample. The first column of dtreevote contains the number of runs for which each feature was used which can be used for feature selection. The first column of ongoingginis contains the cumulative Gini index for each feature across the 100 runs which can be used for feature selection.

Examples

runallmodels(
  num_runs=5,
  num_trees=5,
  kernel='linear',
  poly=0,
  file_path=paste(system.file('samples/subsamples', package = "feamiR"),'/sample',sep=''))
#> $resultdf
#>    model  accuracy sensitivity specificity  type
#> 1  dtree 0.9077844   0.9685230   0.8483412 train
#> 2  dtree 0.8453039   0.9684211   0.7093023  test
#> 3  dtree 0.8957055   0.9620253   0.8333333 train
#> 4  dtree 0.9154229   0.9734513   0.8409091  test
#> 5  dtree 0.9022277   0.9116162   0.8932039 train
#> 6  dtree 0.9086538   0.9375000   0.8750000  test
#> 7  dtree 0.9079284   0.9397906   0.8775000 train
#> 8  dtree 0.9102564   0.9761905   0.8333333  test
#> 9  dtree 0.8937947   0.9549763   0.8317308 train
#> 10 dtree 0.8651685   0.9186047   0.8152174  test
#> 11    rf 0.9461078   0.0000000   0.8933649 train
#> 12    rf 0.8784530   0.0000000   0.7441860  test
#> 13    rf 0.9312883   0.9822785   0.8833333 train
#> 14    rf 0.9004975   0.9469027   0.8409091  test
#> 15    rf 0.9418317   0.9797980   0.9053398 train
#> 16    rf 0.9086538   0.9821429   0.8229167  test
#> 17    rf 0.9322251   0.9738220   0.8925000 train
#> 18    rf 0.9358974   0.0000000   0.8611111  test
#> 19    rf 0.9367542   0.9976303   0.8750000 train
#> 20    rf 0.9325843   0.0000000   0.8695652  test
#> 21   svm 0.9413174   0.9830508   0.9004739 train
#> 22   svm 0.8784530   0.9894737   0.7558140  test
#> 23   svm 0.9226994   0.9746835   0.8738095 train
#> 24   svm 0.9154229   0.9823009   0.8295455  test
#> 25   svm 0.9294554   0.9494949   0.9101942 train
#> 26   svm 0.9230769   0.9821429   0.8541667  test
#> 27   svm 0.9360614   0.9764398   0.8975000 train
#> 28   svm 0.9145299   0.0000000   0.8148148  test
#> 29   svm 0.9260143   0.9834123   0.8677885 train
#> 30   svm 0.9157303   0.9883721   0.8478261  test
#> 
#> $dtreevote
#>                X1 X2 X3 X4 X5 X6
#> classification  0 NA NA NA NA NA
#> position1_A     0 NA NA NA NA NA
#> position1_C     0 NA NA NA NA NA
#> position1_G     0 NA NA NA NA NA
#> position1_U     4  2  3 NA  3  3
#> position2_A     1 NA NA NA  2 NA
#> position2_C     2  7 NA NA  8 NA
#> position2_G     0 NA NA NA NA NA
#> position2_U     0 NA NA NA NA NA
#> position3_A     0 NA NA NA NA NA
#> position3_C     0 NA NA NA NA NA
#> position3_G     0 NA NA NA NA NA
#> position3_U     1 NA NA  5 NA NA
#> position4_A     0 NA NA NA NA NA
#> position4_C     0 NA NA NA NA NA
#> position4_G     2 NA NA NA  5  6
#> position4_U     2 NA  6  6 NA NA
#> position5_A     3 NA NA  5  3  4
#> position5_C     0 NA NA NA NA NA
#> position5_G     0 NA NA NA NA NA
#> position5_U     4  2  2  2 NA  2
#> position6_A     2  4 NA NA NA  3
#> position6_C     0 NA NA NA NA NA
#> position6_G     0 NA NA NA NA NA
#> position6_U     0 NA NA NA NA NA
#> position7_A     0 NA NA NA NA NA
#> position7_C     1 NA NA  8 NA NA
#> position7_G     1  5 NA NA NA NA
#> position7_U     0 NA NA NA NA NA
#> position8_A     0 NA NA NA NA NA
#> position8_C     0 NA NA NA NA NA
#> position8_G     1 NA  7 NA NA NA
#> position8_U     0 NA NA NA NA NA
#> pair1_AA        0 NA NA NA NA NA
#> pair1_AC        0 NA NA NA NA NA
#> pair1_AG        0 NA NA NA NA NA
#> pair1_AU        2 NA NA NA  6  8
#> pair1_CA        0 NA NA NA NA NA
#> pair1_CC        0 NA NA NA NA NA
#> pair1_CG        0 NA NA NA NA NA
#> pair1_CU        0 NA NA NA NA NA
#> pair1_GA        0 NA NA NA NA NA
#> pair1_GC        0 NA NA NA NA NA
#> pair1_GG        0 NA NA NA NA NA
#> pair1_GU        0 NA NA NA NA NA
#> pair1_UA        2 NA NA  4 NA  4
#> pair1_UC        0 NA NA NA NA NA
#> pair1_UG        1 NA NA  4 NA NA
#> pair1_UU        0 NA NA NA NA NA
#> pair2_AA        0 NA NA NA NA NA
#> pair2_AC        0 NA NA NA NA NA
#> pair2_AG        0 NA NA NA NA NA
#> pair2_AU        0 NA NA NA NA NA
#> pair2_CA        0 NA NA NA NA NA
#> pair2_CC        0 NA NA NA NA NA
#> pair2_CG        1 NA NA NA  8 NA
#> pair2_CU        0 NA NA NA NA NA
#> pair2_GA        3 NA  5 NA  4  5
#> pair2_GC        0 NA NA NA NA NA
#> pair2_GG        1 NA NA NA NA  7
#> pair2_GU        1 NA NA  3 NA NA
#> pair2_UA        0 NA NA NA NA NA
#> pair2_UC        0 NA NA NA NA NA
#> pair2_UG        0 NA NA NA NA NA
#> pair2_UU        0 NA NA NA NA NA
#> pair3_AA        0 NA NA NA NA NA
#> pair3_AC        2 NA NA NA  2  2
#> pair3_AG        1 NA NA  5 NA NA
#> pair3_AU        0 NA NA NA NA NA
#> pair3_CA        0 NA NA NA NA NA
#> pair3_CC        0 NA NA NA NA NA
#> pair3_CG        0 NA NA NA NA NA
#> pair3_CU        0 NA NA NA NA NA
#> pair3_GA        1 NA NA NA  5 NA
#> pair3_GC        0 NA NA NA NA NA
#> pair3_GG        0 NA NA NA NA NA
#> pair3_GU        0 NA NA NA NA NA
#> pair3_UA        0 NA NA NA NA NA
#> pair3_UC        2 NA NA NA  7  9
#> pair3_UG        0 NA NA NA NA NA
#> pair3_UU        0 NA NA NA NA NA
#> pair4_AA        1 NA  4 NA NA NA
#> pair4_AC        0 NA NA NA NA NA
#> pair4_AG        0 NA NA NA NA NA
#> pair4_AU        0 NA NA NA NA NA
#> pair4_CA        2  6  6 NA NA NA
#> pair4_CC        0 NA NA NA NA NA
#> pair4_CG        2 NA  2  2 NA NA
#> pair4_CU        0 NA NA NA NA NA
#> pair4_GA        0 NA NA NA NA NA
#> pair4_GC        0 NA NA NA NA NA
#> pair4_GG        0 NA NA NA NA NA
#> pair4_GU        1 NA NA  7 NA NA
#> pair4_UA        0 NA NA NA NA NA
#> pair4_UC        0 NA NA NA NA NA
#> pair4_UG        0 NA NA NA NA NA
#> pair4_UU        0 NA NA NA NA NA
#> pair5_AA        0 NA NA NA NA NA
#> pair5_AC        0 NA NA NA NA NA
#> pair5_AG        1  3 NA NA NA NA
#> pair5_AU        1  6 NA NA NA NA
#> pair5_CA        0 NA NA NA NA NA
#> pair5_CC        0 NA NA NA NA NA
#> pair5_CG        0 NA NA NA NA NA
#> pair5_CU        0 NA NA NA NA NA
#> pair5_GA        0 NA NA NA NA NA
#> pair5_GC        1 NA NA NA  1 NA
#> pair5_GG        0 NA NA NA NA NA
#> pair5_GU        1  3 NA NA NA NA
#> pair5_UA        0 NA NA NA NA NA
#> pair5_UC        0 NA NA NA NA NA
#> pair5_UG        0 NA NA NA NA NA
#> pair5_UU        0 NA NA NA NA NA
#> pair6_AA        0 NA NA NA NA NA
#> pair6_AC        0 NA NA NA NA NA
#> pair6_AG        0 NA NA NA NA NA
#> pair6_AU        0 NA NA NA NA NA
#> pair6_CA        0 NA NA NA NA NA
#> pair6_CC        0 NA NA NA NA NA
#> pair6_CG        0 NA NA NA NA NA
#> pair6_CU        4  4  3  3 NA  3
#> pair6_GA        0 NA NA NA NA NA
#> pair6_GC        2 NA  6  6 NA NA
#> pair6_GG        0 NA NA NA NA NA
#> pair6_GU        0 NA NA NA NA NA
#> pair6_UA        0 NA NA NA NA NA
#> pair6_UC        0 NA NA NA NA NA
#> pair6_UG        0 NA NA NA NA NA
#> pair6_UU        0 NA NA NA NA NA
#> pair7_AA        0 NA NA NA NA NA
#> pair7_AC        4  1  1  1 NA  1
#> pair7_AG        0 NA NA NA NA NA
#> pair7_AU        0 NA NA NA NA NA
#> pair7_CA        0 NA NA NA NA NA
#> pair7_CC        0 NA NA NA NA NA
#> pair7_CG        0 NA NA NA NA NA
#> pair7_CU        0 NA NA NA NA NA
#> pair7_GA        0 NA NA NA NA NA
#> pair7_GC        0 NA NA NA NA NA
#> pair7_GG        0 NA NA NA NA NA
#> pair7_GU        1 NA  5 NA NA NA
#> pair7_UA        0 NA NA NA NA NA
#> pair7_UC        0 NA NA NA NA NA
#> pair7_UG        1 NA NA NA  4 NA
#> pair7_UU        0 NA NA NA NA NA
#> 
#> $ongoingginis
#>                         X1          X2          X3           X4           X5
#> classification  0.00000000          NA          NA           NA           NA
#> position1_A    12.64026130  4.13762336  4.26067029  0.424936121  1.232588523
#> position1_C     8.51435098  0.31165744  0.14423077  3.897984982  0.000000000
#> position1_G    26.49912567  0.17500000  4.99309224  6.656925614  5.488036897
#> position1_U    28.83329043  5.87697694  5.63746338  6.441051651  5.696169491
#> position2_A    34.19049134  3.98880924 22.20819203  1.407797066  1.930529392
#> position2_C     8.00029282  1.85500169  1.55009626  3.614618580  0.029059829
#> position2_G    12.18823006  6.43388108  1.18030303  0.412335601  3.374018045
#> position2_U    13.09073764  2.88178370  3.07551190  0.720526316  0.291301730
#> position3_A    13.19933069  1.03784898  2.90322213  0.857464252  6.614825046
#> position3_C    14.93057876  0.65928030  0.01973684  3.292793172  5.268067738
#> position3_G    12.74305053  3.73209128  0.00000000  6.055403695  0.000000000
#> position3_U    19.34029711  1.96687088  1.63142857  4.033907102  6.121708371
#> position4_A    17.91446110  2.05216816  5.87852715  4.412004340  0.657933275
#> position4_C    21.29081355 11.23513770  7.35606109  0.671811713  0.161373737
#> position4_G    12.72706679  0.79374463  1.63036686  0.513765218  0.000000000
#> position4_U    11.85430113  2.72439196  4.52996909  1.597213897  1.986239293
#> position5_A    60.54814415 12.56414927 12.26848227 15.168052760  3.243693780
#> position5_C    15.01932467  6.47233268  0.06857143  7.339686100  0.488687783
#> position5_G    61.87965558  2.08273916 17.80694362 17.989003619  5.218938781
#> position5_U    38.07735328 11.39938012  1.14078947  4.035738764  9.164853454
#> position6_A    28.84033398 14.16717449  1.96812074  4.634653338  2.947491432
#> position6_C    53.17210145  6.08820439 17.73378017  9.983600952  3.979683686
#> position6_G    20.45659932  8.99874504  5.56937275  4.637058638  1.250842491
#> position6_U    16.69968037  9.11821778  4.91781752  1.041209165  0.000000000
#> position7_A    14.19383360  1.32369179  2.03329905  4.011857363  0.120000000
#> position7_C     8.06365320  4.67842178  0.26722078  0.492307692  2.492369620
#> position7_G    15.62978619  6.06746956  5.12745926  4.195916810  0.203208556
#> position7_U    10.67843406  3.71063539  1.08111763  0.000000000  2.447210555
#> position8_A    22.36919145  2.84823282  3.20285558  4.731743715  4.437005915
#> position8_C    13.94104125  9.14587592  0.07984405  2.313793886  0.104472050
#> position8_G    17.16723416  5.17824432  2.99353236  0.579190627  5.078928235
#> position8_U    13.99969971  3.25166644  0.38620690  3.213201236  6.276716933
#> pair1_AA        5.02093436  0.37333333  0.58910384  2.649870660  1.233719807
#> pair1_AC        2.88275118  0.61490196  2.07272727  0.000000000  0.195121951
#> pair1_AG        0.41896552  0.00000000  0.41896552  0.000000000  0.000000000
#> pair1_AU        5.88747103  1.11471275  0.03809524  3.851453423  0.000000000
#> pair1_CA        0.20991444  0.07843137  0.00000000  0.020242915  0.087681159
#> pair1_CC        2.22911497  2.22911497  0.00000000  0.000000000  0.000000000
#> pair1_CG        0.30788264  0.28928571  0.00000000  0.000000000  0.018596928
#> pair1_CU        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair1_GA        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair1_GC        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair1_GG        0.53333333  0.00000000  0.00000000  0.000000000  0.533333333
#> pair1_GU        1.86962460  0.00000000  1.86962460  0.000000000  0.000000000
#> pair1_UA       16.72109787  4.49014052  6.88368531  0.400000000  0.880440281
#> pair1_UC       14.72269610  6.69093035  4.32870529  0.000000000  1.225416895
#> pair1_UG       18.60224275  3.67898646  4.19426729  7.203933257  0.841493880
#> pair1_UU        7.32097064  5.67699252  0.07619048  1.190009868  0.324444444
#> pair2_AA       15.85229154  0.75811477  2.72388136  4.048591084  5.649131813
#> pair2_AC        0.35539112  0.35539112  0.00000000  0.000000000  0.000000000
#> pair2_AG        2.01056353  0.00000000  0.00000000  2.010563534  0.000000000
#> pair2_AU       62.60928652 11.58065144 17.45478397 13.668530657 10.318554597
#> pair2_CA        0.87610154  0.00000000  0.00000000  0.000000000  0.650537634
#> pair2_CC        1.09817158  0.42424242  0.00000000  0.000000000  0.673929158
#> pair2_CG       10.33405998  2.86666667  0.79079590  3.081389798  3.166116700
#> pair2_CU        4.36462580  1.44175879  1.78981685  0.000000000  0.356241981
#> pair2_GA       22.25344390  2.93255800  1.55977734  6.627359165  8.775224018
#> pair2_GC        0.53434343  0.00000000  0.53434343  0.000000000  0.000000000
#> pair2_GG       18.88202681  0.00000000  4.90160394  0.000000000  7.344139341
#> pair2_GU        0.99388465  0.00000000  0.37267081  0.621213840  0.000000000
#> pair2_UA        6.41275351  0.62060606  0.56576441  0.857142857  1.444048854
#> pair2_UC        0.37333333  0.00000000  0.00000000  0.373333333  0.000000000
#> pair2_UG        2.78884154  0.00000000  0.06666667  1.909616519  0.000000000
#> pair2_UU        4.46144241  0.42724652  1.28920635  0.000000000  2.467480383
#> pair3_AA        4.32711230  0.69750000  0.30421053  2.960960198  0.364441580
#> pair3_AC       64.57912746 11.85195377  4.43341790 14.848777168 21.066331586
#> pair3_AG        7.92413645  2.25560976  0.00000000  0.197509158  1.870174860
#> pair3_AU        7.26094166  2.00186480  1.99617251  0.000000000  3.262904353
#> pair3_CA        2.46171355  2.02957069  0.00000000  0.000000000  0.432142857
#> pair3_CC        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair3_CG        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair3_CU        4.00320447  1.93869431  0.10384615  0.000000000  0.000000000
#> pair3_GA       15.24316685  8.18180031  0.00000000  0.400000000  5.543002607
#> pair3_GC        6.01190971  3.05162781  0.00000000  0.495428571  0.000000000
#> pair3_GG        8.18294911  0.00000000  0.49972738  3.269854797  3.786396569
#> pair3_GU        0.63902320  0.00000000  0.13986014  0.266666667  0.066666667
#> pair3_UA       11.70725135  0.97515053  1.05507246  0.000000000  5.250216895
#> pair3_UC        7.95642551  0.86538462  1.84661183  0.620095694  1.446249618
#> pair3_UG        6.19312361  0.29086538  1.02456140  0.263529412  3.942652780
#> pair3_UU       25.39243359  0.00000000  1.42741582  7.485802918 10.331554027
#> pair4_AA       35.00994611  1.34476011 14.81745203  2.256410256  4.829824420
#> pair4_AC        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair4_AG       13.60250330  0.41689866  1.96863143  6.732193075  1.520962529
#> pair4_AU       19.51373491  6.58859560  0.92132482  7.076118592  3.408742004
#> pair4_CA        5.16983443  0.68342632  0.00000000  0.000000000  1.231701933
#> pair4_CC        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair4_CG       48.95687621  0.79395604 15.50388891 12.051881854 14.208032728
#> pair4_CU        1.58079797  0.00000000  0.01261084  0.785964912  0.160000000
#> pair4_GA        2.56056210  0.36711864  1.21225405  0.751304348  0.000000000
#> pair4_GC        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair4_GG        5.13236703  0.60400746  0.52214452  0.086067019  2.378762356
#> pair4_GU        2.35756551  1.48694411  0.26666667  0.000000000  0.059510286
#> pair4_UA       10.85079353  4.85741711  0.33548387  0.584409938  2.385064923
#> pair4_UC        1.50416020  0.00000000  0.00000000  0.442264914  0.055242967
#> pair4_UG       37.80205226  3.29023318 11.45379859 11.730671592  1.979986050
#> pair4_UU        1.26572106  0.05000000  0.00000000  0.214285714  0.050000000
#> pair5_AA        5.96444706  0.00000000  0.16666667  2.531744500  0.000000000
#> pair5_AC        3.71884389  0.00000000  2.95409491  0.000000000  0.000000000
#> pair5_AG       32.91455839 13.70816317  7.38753338  0.000000000 11.157097145
#> pair5_AU        7.71691178  2.36813439  0.53277488  0.092727273  4.723275245
#> pair5_CA        0.93103448  0.00000000  0.93103448  0.000000000  0.000000000
#> pair5_CC        1.84759338  1.84759338  0.00000000  0.000000000  0.000000000
#> pair5_CG        1.63501864  0.00000000  0.89019105  0.744827586  0.000000000
#> pair5_CU        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair5_GA        1.51504078  1.30246216  0.21257862  0.000000000  0.000000000
#> pair5_GC       41.28846532 15.56319179  0.72368421  0.585799320 18.826971589
#> pair5_GG        6.15574360  0.79764167  0.00000000  0.000000000  1.376572505
#> pair5_GU       14.23754372  5.00953560  0.86179078  6.634816370  1.731400966
#> pair5_UA        3.49901158  1.69958301  1.53344567  0.034871795  0.231111111
#> pair5_UC        3.11833212  1.77823196  0.00000000  0.019862069  0.000000000
#> pair5_UG        5.04243481  0.31515152  0.02142857  0.000000000  3.260381609
#> pair5_UU       12.94663332  2.06925319  2.08480237  3.025366300  3.508323334
#> pair6_AA        2.20930091  1.86970495  0.00000000  0.339595960  0.000000000
#> pair6_AC        0.31103641  0.21960784  0.00000000  0.000000000  0.000000000
#> pair6_AG        7.58712266  3.18905983  0.00000000  0.698181818  1.007441860
#> pair6_AU        3.01737009  0.00000000  0.17102328  2.328398087  0.184615385
#> pair6_CA       15.57674678  0.00000000  0.00000000  4.207244227  9.527381140
#> pair6_CC        0.86812522  0.00000000  0.00000000  0.003047619  0.000000000
#> pair6_CG        0.10000000  0.00000000  0.00000000  0.100000000  0.000000000
#> pair6_CU       30.13439581  3.99819914  4.33007127  9.633930088  9.025262418
#> pair6_GA       10.74703455  5.25299210  3.21409027  2.279952186  0.000000000
#> pair6_GC        7.83166652  1.51071720  0.20484848  3.125857550  2.990243288
#> pair6_GG        1.45113637  0.19342105  0.05369440  1.196878055  0.007142857
#> pair6_GU        6.59528968  0.00000000  3.67719940  1.871716501  0.369230769
#> pair6_UA       22.05307495  6.49251106  9.57655016  2.019242231  1.964912281
#> pair6_UC        1.49562600  0.00000000  0.00000000  0.000000000  1.495625995
#> pair6_UG        4.62761219  1.07267399  0.00000000  2.646295221  0.360962567
#> pair6_UU        3.70418080  3.70418080  0.00000000  0.000000000  0.000000000
#> pair7_AA       13.17232640  0.46730769  0.00000000  3.296818426  5.210682109
#> pair7_AC       24.39595368  5.92630291  3.83329148  4.585328119  3.108803405
#> pair7_AG        8.80103505  1.94620429  3.64074053  1.840952381  0.119486768
#> pair7_AU       11.04457826  1.32831116  3.16715554  5.142089309  1.046925332
#> pair7_CA        0.04927536  0.00000000  0.00000000  0.000000000  0.049275362
#> pair7_CC        0.40000000  0.40000000  0.00000000  0.000000000  0.000000000
#> pair7_CG        0.01018519  0.00000000  0.01018519  0.000000000  0.000000000
#> pair7_CU        5.84291592  0.00000000  3.20179005  2.050967742  0.207428571
#> pair7_GA        6.22529573  0.00000000  0.24000000  1.062388592  0.086041083
#> pair7_GC        0.00000000  0.00000000  0.00000000  0.000000000  0.000000000
#> pair7_GG        0.84607265  0.00000000  0.54680794  0.087500000  0.000000000
#> pair7_GU       19.36125812  4.96253705  9.63898577  1.977607143  1.726342711
#> pair7_UA        4.22688632  0.71018781  1.78953634  0.806666667  0.913846154
#> pair7_UC        2.07755828  0.00000000  0.00000000  1.992331002  0.000000000
#> pair7_UG       24.18962420  3.59138892  2.42822389 10.054840283  2.295702889
#> pair7_UU       12.02719793  1.46881582  5.21650609  2.813238095  0.150300329
#>                          X6
#> classification           NA
#> position1_A    2.584443e+00
#> position1_C    4.160478e+00
#> position1_G    9.186071e+00
#> position1_U    5.181629e+00
#> position2_A    4.655164e+00
#> position2_C    9.515165e-01
#> position2_G    7.876923e-01
#> position2_U    6.121614e+00
#> position3_A    1.785970e+00
#> position3_C    5.690701e+00
#> position3_G    2.955556e+00
#> position3_U    5.586382e+00
#> position4_A    4.913828e+00
#> position4_C    1.866429e+00
#> position4_G    9.789190e+00
#> position4_U    1.016487e+00
#> position5_A    1.730377e+01
#> position5_C    6.500467e-01
#> position5_G    1.878203e+01
#> position5_U    1.233659e+01
#> position6_A    5.122894e+00
#> position6_C    1.538683e+01
#> position6_G    5.804066e-04
#> position6_U    1.622436e+00
#> position7_A    6.704985e+00
#> position7_C    1.333333e-01
#> position7_G    3.573201e-02
#> position7_U    3.439470e+00
#> position8_A    7.149353e+00
#> position8_C    2.297055e+00
#> position8_G    3.337339e+00
#> position8_U    8.719082e-01
#> pair1_AA       1.749067e-01
#> pair1_AC       0.000000e+00
#> pair1_AG       0.000000e+00
#> pair1_AU       8.832096e-01
#> pair1_CA       2.355900e-02
#> pair1_CC       0.000000e+00
#> pair1_CG       0.000000e+00
#> pair1_CU       0.000000e+00
#> pair1_GA       0.000000e+00
#> pair1_GC       0.000000e+00
#> pair1_GG       0.000000e+00
#> pair1_GU       0.000000e+00
#> pair1_UA       4.066832e+00
#> pair1_UC       2.477644e+00
#> pair1_UG       2.683562e+00
#> pair1_UU       5.333333e-02
#> pair2_AA       2.672573e+00
#> pair2_AC       0.000000e+00
#> pair2_AG       0.000000e+00
#> pair2_AU       9.586766e+00
#> pair2_CA       2.255639e-01
#> pair2_CC       0.000000e+00
#> pair2_CG       4.290909e-01
#> pair2_CU       7.768082e-01
#> pair2_GA       2.358525e+00
#> pair2_GC       0.000000e+00
#> pair2_GG       6.636284e+00
#> pair2_GU       0.000000e+00
#> pair2_UA       2.925191e+00
#> pair2_UC       0.000000e+00
#> pair2_UG       8.125584e-01
#> pair2_UU       2.775092e-01
#> pair3_AA       0.000000e+00
#> pair3_AC       1.237865e+01
#> pair3_AG       3.600843e+00
#> pair3_AU       0.000000e+00
#> pair3_CA       0.000000e+00
#> pair3_CC       0.000000e+00
#> pair3_CG       0.000000e+00
#> pair3_CU       1.960664e+00
#> pair3_GA       1.118364e+00
#> pair3_GC       2.464853e+00
#> pair3_GG       6.269704e-01
#> pair3_GU       1.658297e-01
#> pair3_UA       4.426811e+00
#> pair3_UC       3.178084e+00
#> pair3_UG       6.715146e-01
#> pair3_UU       6.147661e+00
#> pair4_AA       1.176150e+01
#> pair4_AC       0.000000e+00
#> pair4_AG       2.963818e+00
#> pair4_AU       1.518954e+00
#> pair4_CA       3.254706e+00
#> pair4_CC       0.000000e+00
#> pair4_CG       6.399117e+00
#> pair4_CU       6.222222e-01
#> pair4_GA       2.298851e-01
#> pair4_GC       0.000000e+00
#> pair4_GG       1.541386e+00
#> pair4_GU       5.444444e-01
#> pair4_UA       2.688418e+00
#> pair4_UC       1.006652e+00
#> pair4_UG       9.347363e+00
#> pair4_UU       9.514353e-01
#> pair5_AA       3.266036e+00
#> pair5_AC       7.647490e-01
#> pair5_AG       6.617647e-01
#> pair5_AU       0.000000e+00
#> pair5_CA       0.000000e+00
#> pair5_CC       0.000000e+00
#> pair5_CG       0.000000e+00
#> pair5_CU       0.000000e+00
#> pair5_GA       0.000000e+00
#> pair5_GC       5.588818e+00
#> pair5_GG       3.981529e+00
#> pair5_GU       0.000000e+00
#> pair5_UA       0.000000e+00
#> pair5_UC       1.320238e+00
#> pair5_UG       1.445473e+00
#> pair5_UU       2.258888e+00
#> pair6_AA       0.000000e+00
#> pair6_AC       9.142857e-02
#> pair6_AG       2.692439e+00
#> pair6_AU       3.333333e-01
#> pair6_CA       1.842121e+00
#> pair6_CC       8.650776e-01
#> pair6_CG       0.000000e+00
#> pair6_CU       3.146933e+00
#> pair6_GA       0.000000e+00
#> pair6_GC       0.000000e+00
#> pair6_GG       0.000000e+00
#> pair6_GU       6.771430e-01
#> pair6_UA       1.999859e+00
#> pair6_UC       0.000000e+00
#> pair6_UG       5.476804e-01
#> pair6_UU       0.000000e+00
#> pair7_AA       4.197518e+00
#> pair7_AC       6.942228e+00
#> pair7_AG       1.253651e+00
#> pair7_AU       3.600969e-01
#> pair7_CA       0.000000e+00
#> pair7_CC       0.000000e+00
#> pair7_CG       0.000000e+00
#> pair7_CU       3.827296e-01
#> pair7_GA       4.836866e+00
#> pair7_GC       0.000000e+00
#> pair7_GG       2.117647e-01
#> pair7_GU       1.055785e+00
#> pair7_UA       6.649351e-03
#> pair7_UC       8.522727e-02
#> pair7_UG       5.819468e+00
#> pair7_UU       2.378338e+00
#>