as.data.frame.pareg | as.data.frame for an object of class 'pareg'. |
as_dense_sim | Convert matrices. |
as_enrichplot_object | Convert object of class 'pareg' to class 'enrichResult'. |
bernoulli | Family objects for models |
beta | Family objects for models |
beta_phi_lm | Family objects for models |
beta_phi_var | Family objects for models |
compute_term_similarities | Term similarity computation. |
create_model_df | Create design matrix. |
cv_edgenet | Find the optimal shrinkage parameters for edgenet |
cv_edgenet-method | Find the optimal shrinkage parameters for edgenet |
edgenet | Fit a graph-regularized linear regression model using edge-based regularization. Adapted from https://github.com/dirmeier/netReg. |
edgenet-method | Fit a graph-regularized linear regression model using edge-based regularization. Adapted from https://github.com/dirmeier/netReg. |
family | Family objects for models |
gaussian | Family objects for models |
generate_similarity_matrix | Similarity matrix generation. |
jaccard | Jaccard similarity. |
overlap_coefficient | Overlap coefficient. |
pareg | Pathway enrichment using a regularized regression approach. |
pathway_similarities | Collection of pathway similarity matrices. |
plot.pareg | Plot pareg object. |
plot_pareg_with_args | Plot result of enrichment computation. |
similarity_sample | Sample elements based on similarity structure. |
transform_y | Transform vector from [0, 1] to (0, 1). |