# Pathway enrichment using a regularized regression approach

## Documentation for package ‘pareg’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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).