# LUCID with Multiple Omics Data

## Documentation for package ‘LUCIDus’ version 3.2.1

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

## Help Pages

analyze_missing_pattern | Describe the missing-data pattern of an omics matrix
boot_lucid | Inference of LUCID model based on bootstrap resampling
check_imputation_quality | Check whether imputed values are distributionally plausible
check_na | Classify each subject's omics missingness pattern
estimate_lucid | Fit LUCID models with one or multiple omics layers
get_cluster_assignment | Extract the hard cluster assignment from a fitted LUCID model
get_selected_G | Extract selected (retained) exposures from a fitted LUCID model
get_selected_Z | Extract selected (retained) omics features from a fitted LUCID model
get_top_omics_features | Extract the top-N most important omics features from a fitted LUCID model
lucid | Fit a lucid model for integrated analysis on exposure, outcome and multi-omics data, allowing for tuning
plot.early_lucid | Visualize an early-integration LUCID model through a Sankey diagram
plot.lucid_parallel | Sankey diagram for a parallel-integration LUCID model (not yet implemented)
plot.lucid_serial | Sankey diagram for a serial-integration LUCID model (not yet implemented)
plot_cluster_omic_profile | Plot per-cluster omics profiles
predict_lucid | Predict Cluster Assignment and Outcome From a Fitted LUCID Model
print.sumlucid_early | Print the output of LUCID in a nicer table
print.sumlucid_parallel | Print the output of LUCID in a nicer table
print.sumlucid_serial | Print the output of LUCID in a nicer table
safe_impute | Single-value imputation that tolerates fully missing columns
simulated_HELIX_data | A simulated HELIX dataset for LUCID
sim_data | A simulated dataset for LUCID
summary.early_lucid | Summarize results of the early LUCID model
summary.lucid_parallel | Summarize results of the parallel LUCID model
summary.lucid_serial | Summarize results of the serial LUCID model
summary_lucid | Summarize results of the early LUCID model
tune_lucid | Wrapper for LUCID Model and Penalty Tuning