# 'C++' Implementations of Functional Enrichment Analysis

## Documentation for package ‘enrichit’ version 0.2.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

aggregate_enrichment | Aggregate multiple enrichment results (Late Fusion)
aggregate_omics | Aggregate multi-omics gene/protein-level statistics
bayes_enrich | Bayesian term selection for enrichment results
bayes_summary | Summarize Bayesian enrichment results
classify_omics_pattern | Classify pathway-level multi-omics patterns
collapse_multilayer_scores | Collapse multi-layer diffusion scores
compareClusterResult-class | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
enrichit_params | Common parameters for enrichit functions
enrichResult-class | Class "enrichResult" This class represents the result of enrichment analysis.
EXTID2NAME | EXTID2NAME
extract_mnsea_subnetwork | Extract pathway subnetwork data from a 'mnseaResult'
geneID | geneID generic
geneInCategory | geneInCategory generic
get_mnsea_contribution | Get cached contribution tables from a 'mnseaResult'
get_omics_contribution | Get gene-level omics contribution for a specific pathway
gsea | Gene Set Enrichment Analysis (GSEA)
gseahResult-class | Class "gseaResult" This class represents the result of GSEA analysis
gseaResult-class | Class "gseaResult" This class represents the result of GSEA analysis
gseaScores | Calculate GSEA Running Enrichment Scores
gsea_gson | gsea_gson
gsfilter | gsfilter
harmonize_ids | Harmonize feature IDs to a target space
mnsea | Multi-layer Network-based Gene Set Enrichment Analysis
mnseaResult-class | Class "mnseaResult" This class represents the result of multi-layer Network-based Set Enrichment Analysis.
mnsea_gson | Multi-layer NSEA using a GSON object
nsea | Network-based Gene Set Enrichment Analysis
nseaResult-class | Class "nseaResult" This class represents the result of Network-based Set Enrichment Analysis (NSEA).
nsea_gson | Network-based GSEA using a GSON object
ora | Over-Representation Analysis (ORA)
ora_gson | ora-gson
plot-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
prepare_multilayer_network | Prepare multi-layer network for repeated propagation
prepare_network | Prepare network for repeated NSEA runs
propagate_multilayer | Propagate signals on a multi-layer network
select_features_for_ora | Select features for ORA
setReadable | setReadable
show | show method
show-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
show-method | Class "enrichResult" This class represents the result of enrichment analysis.
show-method | Class "gseaResult" This class represents the result of GSEA analysis
show-method | show method
summary | summary method
summary-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
summary-method | Class "enrichResult" This class represents the result of enrichment analysis.
summary-method | Class "gseaResult" This class represents the result of GSEA analysis