diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index cbe9063..97e7ffe 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -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 @@ -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 }} diff --git a/README.md b/README.md index 114f4fc..6b0cd20 100644 --- a/README.md +++ b/README.md @@ -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 @@ -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 @@ -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 © 2024 Institute of Medical Biometry and Statistics (IMBS). 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