Pathway enrichment using a regularized regression approach

Documentation for package ‘pareg’ version 1.9.0

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
cluster_apply	Parallelize function calls on LSF cluster.
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.
pareg_env	Conda environment definition.
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).