imirage.cv.loop.RdConvinient wrapper for imirage.cv that performs cross-validation analysis for assessing imputation accuracies for all miRNAs using the training datasets
imirage.cv.loop(train_pcg, train_mir, method = "KNN", ...)
| train_pcg | training protein coding dataset. a numeric matrix with with row names indicating samples, and column names indicating protein coding gene IDs. |
|---|---|
| train_mir | training miRNA expression dataset. a numeric matrix with row names indicating samples, and column names indicating miRNA IDs. |
| method | method for imputation, either "RF" for random forests, "KNN" for K-nearest neighbor or "SVM" for support vector machines. |
| ... | optional parameters that can be passed on to the machine-learning method: RF (randomForest), KNN (knn.reg) or SVM(svm) |
a matrix containing Spearman's correlation coefficient, P-value and RMSE from the cross-validation analysis of the complete miRNA training dataset
imirage.cv.loop(train_pcg = GA.pcg, train_mir = GA.mir, method = "KNN")#> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 1 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 2 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 3 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 4 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 5 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 6 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 7 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 8 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 9 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 10 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 11 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 12 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 13 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 14 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 15 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 16 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 17 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 18 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 19 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 20 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 21 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 22 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 23 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 24 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 25#> Coef P-value RMSE #> [1,] 0.7300351 0.0002925290 1697.284363 #> [2,] 0.6653974 0.0014939502 1821.778490 #> [3,] 0.4000387 0.0715835250 42856.733562 #> [4,] 0.6910587 0.0008767788 40224.607322 #> [5,] 0.6383672 0.0014917283 12.524825 #> [6,] 0.6433970 0.0041425052 596.727633 #> [7,] 0.6735154 0.0004133977 29.523679 #> [8,] 0.5446510 0.0240657832 1819.110218 #> [9,] 0.4761614 0.0642250470 195.313273 #> [10,] 0.5437893 0.0212990767 1117.837619 #> [11,] 0.5140531 0.0064255996 451.123657 #> [12,] 0.5602927 0.0384941445 732.258837 #> [13,] 0.6725363 0.0003492255 23.026537 #> [14,] 0.5253185 0.0151291506 32.414151 #> [15,] 0.3126551 0.1843614536 1068.520213 #> [16,] 0.2417694 0.2765782374 127.152286 #> [17,] 0.2509034 0.2802530989 2160.665136 #> [18,] 0.5181730 0.0839872968 278.788337 #> [19,] 0.6576904 0.0195764377 1080.458181 #> [20,] 0.6124201 0.0086183693 26.962239 #> [21,] 0.3974595 0.0765790954 4.351999 #> [22,] 0.6367786 0.0012933732 17.619665 #> [23,] 0.6184743 0.0085029892 3.555302 #> [24,] 0.3769442 0.1471948054 21.378330 #> [25,] 0.6909977 0.0004364099 508.820175imirage.cv.loop(train_pcg = GA.pcg, train_mir = GA.mir, method = "SVM")#> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 1 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 2 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 3 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 4 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 5 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 6 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 7 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 8 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 9 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 10 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 11 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 12 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 13 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 14 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 15 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 16 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 17 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 18 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 19 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 20 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 21 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 22 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 23 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 24 #> #> Running 10-folds cross-validation... #> Iteration 1 #> Iteration 2 #> Iteration 3 #> Iteration 4 #> Iteration 5 #> Iteration 6 #> Iteration 7 #> Iteration 8 #> Iteration 9 #> Iteration 10 #> Cross-validation complete #> [1] 25#> Coef P-value RMSE #> [1,] 0.7104452 0.0004298967 1405.485436 #> [2,] 0.6555322 0.0005283253 1507.732130 #> [3,] 0.2877401 0.2194577547 43317.983971 #> [4,] 0.6473227 0.0050200215 35671.878027 #> [5,] 0.6256337 0.0074740491 13.045980 #> [6,] 0.6677295 0.0005716250 566.987418 #> [7,] 0.5981074 0.0026596816 30.053957 #> [8,] 0.6181647 0.0018363604 1753.804777 #> [9,] 0.5465199 0.0074093743 171.548014 #> [10,] 0.6539363 0.0059528599 981.145659 #> [11,] 0.5398726 0.0193491020 439.360917 #> [12,] 0.5191159 0.0248316013 727.657325 #> [13,] 0.5952436 0.0045855931 21.681466 #> [14,] 0.5964371 0.0051113700 32.236214 #> [15,] 0.4750968 0.0289148202 1018.862281 #> [16,] 0.4194248 0.0710492132 121.985463 #> [17,] 0.4486195 0.0287162855 2167.559305 #> [18,] 0.4757285 0.0341738995 280.934267 #> [19,] 0.6391439 0.0038216609 1078.691534 #> [20,] 0.6148403 0.0077252346 26.598612 #> [21,] 0.4372627 0.0268064233 4.289136 #> [22,] 0.5874615 0.0024403653 17.711760 #> [23,] 0.6145043 0.0035004574 3.317946 #> [24,] 0.3841954 0.1156089391 21.281623 #> [25,] 0.6457354 0.0046491365 400.537564