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@fouodo
fouodo committed Jul 18, 2024
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Expand Up @@ -235,44 +235,47 @@ print(var_sel_res)
## Layer variable
## 1 geneexpr ACACA
## 2 geneexpr BAP1
## 3 geneexpr EIF4E
## 4 geneexpr MAP2K1
## 5 geneexpr PCNA
## 6 geneexpr YWHAE
## 7 proteinexpr Bap1.c.4
## 8 proteinexpr Bid
## 9 proteinexpr Cyclin_E2
## 10 proteinexpr P.Cadherin
## 11 proteinexpr Chk1
## 12 proteinexpr Chk1_pS345
## 13 proteinexpr EGFR
## 14 proteinexpr EGFR_pY1173
## 15 proteinexpr HER3_pY1289
## 16 proteinexpr MIG.6
## 17 proteinexpr ETS.1
## 18 proteinexpr MEK1_pS217_S221
## 19 proteinexpr p38_MAPK
## 20 proteinexpr c.Met_pY1235
## 21 proteinexpr N.Ras
## 22 proteinexpr PCNA
## 23 proteinexpr PEA15_pS116
## 24 proteinexpr PKC.delta_pS664
## 25 proteinexpr Rad50
## 26 proteinexpr C.Raf_pS338
## 27 proteinexpr p70S6K
## 28 proteinexpr p70S6K_pT389
## 29 proteinexpr Smad4
## 30 proteinexpr STAT3_pY705
## 31 proteinexpr 14.3.3_epsilon
## 32 methylation cg20139214
## 33 methylation cg18457775
## 34 methylation cg24747396
## 35 methylation cg01306510
## 36 methylation cg02412050
## 37 methylation cg07566050
## 38 methylation cg20849549
## 39 methylation cg25539131
## 40 methylation cg07064406
## 3 geneexpr CHEK2
## 4 geneexpr EIF4E
## 5 geneexpr MAP2K1
## 6 geneexpr MAPK14
## 7 geneexpr PCNA
## 8 geneexpr YWHAE
## 9 proteinexpr Bap1.c.4
## 10 proteinexpr Bid
## 11 proteinexpr Cyclin_E2
## 12 proteinexpr P.Cadherin
## 13 proteinexpr Chk1
## 14 proteinexpr Chk1_pS345
## 15 proteinexpr EGFR
## 16 proteinexpr EGFR_pY1173
## 17 proteinexpr HER3_pY1289
## 18 proteinexpr MIG.6
## 19 proteinexpr ETS.1
## 20 proteinexpr MEK1_pS217_S221
## 21 proteinexpr p38_MAPK
## 22 proteinexpr c.Met_pY1235
## 23 proteinexpr N.Ras
## 24 proteinexpr PCNA
## 25 proteinexpr PEA15_pS116
## 26 proteinexpr PKC.delta_pS664
## 27 proteinexpr Rad50
## 28 proteinexpr C.Raf_pS338
## 29 proteinexpr p70S6K
## 30 proteinexpr p70S6K_pT389
## 31 proteinexpr Smad4
## 32 proteinexpr STAT3_pY705
## 33 proteinexpr 14.3.3_epsilon
## 34 methylation cg20139214
## 35 methylation cg18457775
## 36 methylation cg24747396
## 37 methylation cg01306510
## 38 methylation cg02412050
## 39 methylation cg07566050
## 40 methylation cg02630105
## 41 methylation cg20849549
## 42 methylation cg25539131
## 43 methylation cg07064406

For each layer, the variable selection results show the chosen
variables. In this example, we perform variable selection on the entire
Expand Down Expand Up @@ -377,9 +380,9 @@ print(model_ge)
## Layer : geneexpr
## ind. id. : IDS
## target : disease
## n : 26
## n : 27
## Missing : 0
## p : 7
## p : 9

#### C) Predicting

Expand Down Expand Up @@ -428,29 +431,29 @@ print(new_predictions)
##
## $predicted_values
## IDS geneexpr proteinexpr methylation meta_layer
## 1 subject4 0.7366615 0.6384437 0.32332937 0.5639329
## 2 subject7 0.6361365 0.2253671 0.58885000 0.4649861
## 3 subject8 0.8359429 0.9122571 0.57208492 0.7783530
## 4 subject10 0.8332671 0.8405218 0.82245556 0.8324714
## 5 subject13 0.7866813 0.2582524 0.15968333 0.3808876
## 6 subject15 0.5889984 0.8418933 0.23018810 0.5671874
## 7 subject16 0.9577306 0.2872087 0.30760516 0.4905130
## 8 subject18 0.8485437 0.1967528 0.01865159 0.3294865
## 9 subject23 0.9654341 0.1157877 0.64309841 0.5378101
## 10 subject24 0.4120274 0.6668254 0.58165516 0.5641876
## 11 subject27 0.1468226 0.2008639 0.40676190 0.2525217
## 12 subject31 0.6630813 0.8202754 0.42525714 0.6446734
## 13 subject32 0.7359627 0.7580425 0.42763452 0.6432427
## 14 subject35 0.3883032 0.7742742 0.74610714 0.6518612
## 15 subject36 0.3309869 0.1619488 0.44883571 0.3055726
## 16 subject50 0.8563032 0.5694786 0.60321230 0.6646439
## 17 subject54 0.6911706 0.7139881 0.91125198 0.7719709
## 18 subject55 0.6768560 0.1810726 0.42335754 0.4058851
## 19 subject59 0.6293425 0.2157679 0.37993492 0.3908631
## 20 subject62 0.2332067 0.1793825 0.28952937 0.2312774
## 21 subject63 0.3095397 0.7660052 0.83139325 0.6535934
## 22 subject66 0.6125536 0.6647683 0.89241111 0.7240907
## 23 subject70 0.6169607 0.2390425 0.27369524 0.3612205
## 1 subject4 0.5729984 0.6283444 0.37592262 0.5238763
## 2 subject7 0.4546028 0.1430000 0.41540397 0.3306247
## 3 subject8 0.6938500 0.8740036 0.58768135 0.7206080
## 4 subject10 0.8614921 0.8670433 0.71899286 0.8137715
## 5 subject13 0.4828944 0.3183373 0.17456349 0.3171327
## 6 subject15 0.6921825 0.8668000 0.43054325 0.6627722
## 7 subject16 0.7396742 0.2816353 0.26842897 0.4132131
## 8 subject18 0.7437706 0.1875627 0.02909325 0.2976783
## 9 subject23 0.7547107 0.2127790 0.57286706 0.4994574
## 10 subject24 0.3501337 0.5554821 0.59494167 0.5081872
## 11 subject27 0.5125694 0.2528040 0.35571071 0.3659174
## 12 subject31 0.5171909 0.8374758 0.52997817 0.6350335
## 13 subject32 0.5383274 0.7887183 0.54169921 0.6281439
## 14 subject35 0.3027032 0.7871099 0.72650159 0.6219553
## 15 subject36 0.5808337 0.1891099 0.46222103 0.4008025
## 16 subject50 0.8612718 0.5800012 0.73700675 0.7183713
## 17 subject54 0.5155119 0.7002710 0.89052937 0.7116772
## 18 subject55 0.5351155 0.2145329 0.49238333 0.4067265
## 19 subject59 0.3558187 0.2316774 0.28723532 0.2879582
## 20 subject62 0.2787401 0.2784730 0.27884127 0.2786808
## 21 subject63 0.2825139 0.7363254 0.85223413 0.6418141
## 22 subject66 0.6464357 0.6408508 0.92384881 0.7411852
## 23 subject70 0.2521048 0.3248405 0.20570397 0.2616752

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