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@fouodo
fouodo committed Jul 18, 2024
1 parent 339b924 commit b180b17
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7 changes: 1 addition & 6 deletions .github/workflows/R-CMD-check.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ jobs:
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

steps:
- uses: actions/checkout@v4
Expand All @@ -50,9 +51,3 @@ jobs:
with:
upload-snapshots: true
build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
- name: Run tests
run: |
Rscript -e 'install.packages("covr");library(covr);codecov(token = Sys.getenv("CODECOV_TOKEN"))'
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
137 changes: 70 additions & 67 deletions README.md
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Expand Up @@ -225,48 +225,51 @@ print(var_sel_res)

## Layer variable
## 1 geneexpr ACACA
## 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 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
## 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

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 @@ -371,9 +374,9 @@ print(model_ge)
## Layer : geneexpr
## ind. id. : IDS
## target : disease
## n : 27
## n : 28
## Missing : 0
## p : 9
## p : 11

#### C) Predicting

Expand Down Expand Up @@ -422,29 +425,29 @@ print(new_predictions)
##
## $predicted_values
## IDS geneexpr proteinexpr methylation meta_layer
## 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
## 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

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