'C++' Implementations of Functional Enrichment Analysis

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Documentation for package ‘enrichit’ version 0.2.0

• DESCRIPTION file
• Package NEWS
• Package README

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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