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@fouodo
fouodo committed Jul 18, 2024
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3 changes: 2 additions & 1 deletion .Rbuildignore
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^\.Rproj\.user$
^.*test_code*
^\.github$
^\.README_files*
^README.Rmd
^README.files
140 changes: 70 additions & 70 deletions README.md
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## Layer variable
## 1 geneexpr ACACA
## 2 geneexpr ASNS
## 3 geneexpr BAP1
## 4 geneexpr CHEK2
## 5 geneexpr EIF4E
## 6 geneexpr MAP2K1
## 7 geneexpr MAPK14
## 8 geneexpr PCNA
## 9 geneexpr SMAD4
## 10 geneexpr YWHAE
## 11 proteinexpr Bap1.c.4
## 12 proteinexpr Bid
## 13 proteinexpr Cyclin_E2
## 14 proteinexpr P.Cadherin
## 15 proteinexpr Chk1
## 16 proteinexpr Chk1_pS345
## 17 proteinexpr EGFR
## 18 proteinexpr EGFR_pY1173
## 19 proteinexpr HER3_pY1289
## 20 proteinexpr MIG.6
## 21 proteinexpr ETS.1
## 22 proteinexpr MEK1_pS217_S221
## 23 proteinexpr p38_MAPK
## 24 proteinexpr c.Met_pY1235
## 25 proteinexpr N.Ras
## 26 proteinexpr PCNA
## 27 proteinexpr PEA15_pS116
## 28 proteinexpr PKC.delta_pS664
## 29 proteinexpr Rad50
## 30 proteinexpr C.Raf_pS338
## 31 proteinexpr p70S6K
## 32 proteinexpr p70S6K_pT389
## 33 proteinexpr Smad4
## 34 proteinexpr STAT3_pY705
## 35 proteinexpr 14.3.3_epsilon
## 36 methylation cg20139214
## 37 methylation cg09637363
## 38 methylation cg01306510
## 39 methylation cg11861730
## 40 methylation cg02412050
## 41 methylation cg07566050
## 42 methylation cg02630105
## 43 methylation cg20849549
## 44 methylation cg00547829
## 45 methylation cg25539131
## 46 methylation cg07064406
## 2 geneexpr BAP1
## 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 PEA15_pS116
## 25 proteinexpr PKC.delta_pS664
## 26 proteinexpr Rad50
## 27 proteinexpr C.Raf_pS338
## 28 proteinexpr p70S6K
## 29 proteinexpr p70S6K_pT389
## 30 proteinexpr Smad4
## 31 proteinexpr STAT3_pY705
## 32 proteinexpr 14.3.3_epsilon
## 33 methylation cg20139214
## 34 methylation cg18457775
## 35 methylation cg24747396
## 36 methylation cg09637363
## 37 methylation cg01306510
## 38 methylation cg02412050
## 39 methylation cg25984124
## 40 methylation cg07566050
## 41 methylation cg02630105
## 42 methylation cg20849549
## 43 methylation cg00547829
## 44 methylation cg25539131
## 45 methylation cg07064406
## 46 methylation cg11816577

For each layer, the variable selection results show the chosen
variables. In this example, we perform variable selection on the entire
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## Layer : geneexpr
## ind. id. : IDS
## target : disease
## n : 28
## n : 24
## Missing : 0
## p : 11
## p : 9

#### C) Predicting

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##
## $predicted_values
## IDS geneexpr proteinexpr methylation meta_layer
## 1 subject4 0.5756151 0.6088821 0.59866151 0.5957997
## 2 subject7 0.5285984 0.1540829 0.37789484 0.3384078
## 3 subject8 0.8418587 0.8724944 0.58340556 0.7651778
## 4 subject10 0.6889532 0.7677829 0.73604286 0.7342206
## 5 subject13 0.5070341 0.2231417 0.15008849 0.2801885
## 6 subject15 0.7497833 0.8700246 0.54204722 0.7236007
## 7 subject16 0.8247607 0.2039111 0.12554325 0.3563938
## 8 subject18 0.7051587 0.3508202 0.03149365 0.3443074
## 9 subject23 0.8315040 0.1438377 0.48493492 0.4584902
## 10 subject24 0.5099313 0.5681544 0.59532460 0.5606064
## 11 subject27 0.3201488 0.1700040 0.36788810 0.2807431
## 12 subject31 0.5710960 0.8110262 0.74740873 0.7201114
## 13 subject32 0.7474405 0.7355480 0.60948968 0.6960397
## 14 subject35 0.4236238 0.8382635 0.53434841 0.6150725
## 15 subject36 0.5315718 0.2164028 0.29057143 0.3326257
## 16 subject50 0.8037694 0.5519028 0.61384841 0.6456929
## 17 subject54 0.7089933 0.6285722 0.81777817 0.7162329
## 18 subject55 0.6680595 0.1546952 0.45363452 0.4046833
## 19 subject59 0.4505107 0.1891437 0.27353810 0.2933226
## 20 subject62 0.3034996 0.3299591 0.18915992 0.2743611
## 21 subject63 0.4179254 0.7647552 0.81445238 0.6815886
## 22 subject66 0.7891885 0.6220889 0.92215437 0.7725282
## 23 subject70 0.3405563 0.3003980 0.28061230 0.3052480
## 1 subject4 0.5692770 0.7216738 0.5381234 0.6120387
## 2 subject7 0.5245984 0.1517905 0.4670440 0.3700894
## 3 subject8 0.7372762 0.9001016 0.6653460 0.7685477
## 4 subject10 0.8185226 0.8399246 0.6433667 0.7608181
## 5 subject13 0.4501103 0.3053063 0.2560587 0.3260454
## 6 subject15 0.6945798 0.9100496 0.4598270 0.6838968
## 7 subject16 0.7228405 0.2317556 0.4113329 0.4313865
## 8 subject18 0.6225540 0.2598992 0.1398702 0.3130737
## 9 subject23 0.7695409 0.1713853 0.6136909 0.4979463
## 10 subject24 0.4136722 0.7267909 0.4837393 0.5515487
## 11 subject27 0.4922226 0.2237667 0.5171135 0.4057083
## 12 subject31 0.4245571 0.8263060 0.4952425 0.5942924
## 13 subject32 0.4240972 0.8565766 0.7284512 0.6919688
## 14 subject35 0.2577560 0.7256048 0.6949587 0.5878086
## 15 subject36 0.4312321 0.1882139 0.5812706 0.4004817
## 16 subject50 0.7175571 0.5257234 0.8015587 0.6804371
## 17 subject54 0.5352171 0.7050111 0.8339952 0.7072681
## 18 subject55 0.5982429 0.2227556 0.3961583 0.3888607
## 19 subject59 0.4251044 0.1941571 0.6051290 0.4098478
## 20 subject62 0.3933698 0.2651238 0.2761345 0.3038700
## 21 subject63 0.5148698 0.8214048 0.8638964 0.7544627
## 22 subject66 0.5892992 0.6357849 0.8877810 0.7172364
## 23 subject70 0.2878270 0.3115385 0.4574508 0.3595667

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