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Example for Survival Data -- Breast Invasive Carcinoma3 years ago
Instalation | Required Packages | Load data | Fit models | Results of Cross Validation | Coefficients of selected model from Cross-Validation | Survival curves and Log rank test | Session Info
glmSparseNet 1.31.0André Veríssimoexample_brca_survival.Rmd
Breast survival dataset using network from STRING DB3 years ago
Instalation | Required Packages | Overview | Download Data from STRING | Build network matrix | Network Statistics | Graph information | Summary of degree (indegree + outdegree) | Histogram of degree (up until 99.999% quantile) | glmSparseNet | Select balanced folds for cross-validation | glmHub model | glmOrphan model | Elastic Net model (without network-penalization) | Selected genes | Session Info
glmSparseNet 1.31.0André Veríssimoexample_brca_protein-protein-interactions_survival.Rmd
Example for Classification Data -- Breast Invasive Carcinoma3 years ago
Instalation | Required Packages | Load data | Fit models | Results of Cross Validation | Coefficients of selected model from Cross-Validation | Accuracy | Session Info
glmSparseNet 1.31.0Marta Lopes and André Veríssimoexample_brca_logistic.Rmd
Example for Survival Data -- Prostate Adenocarcinoma3 years ago
Instalation | Required Packages | Load data | Fit models | Results of Cross Validation | Coefficients of selected model from Cross-Validation | Survival curves and Log rank test | Session Info
glmSparseNet 1.31.0Marta Lopes and André Veríssimoexample_prad_survival.Rmd
Example for Survival Data -- Skin Melanoma3 years ago
Instalation | Required Packages | Load data | Fit models | Results of Cross Validation | Coefficients of selected model from Cross-Validation | Survival curves and Log rank test | Session Info
glmSparseNet 1.31.0Eunice Carrasquinha and André Veríssimoexample_skcm_survival.Rmd
Separate 2 groups in Cox regression3 years ago
Instalation | Required Packages | Prepare data | Separate using age as co-variate | Kaplan-Meier survival results | Plot | Separate using age as co-variate (group cutoff is 40% - 60%) | Separate using age as co-variate (group cutoff is 60% - 40%) | Session Info
glmSparseNet 1.31.0André Veríssimoseparate2GroupsCox.Rmd