Function reference • ReporterScore

All functions
`CPDlist`	The CPDlist used for enrichment.
`Compound_htable`	Compound htable from 'KEGG'
`GOlist`	The GOlist used for enrichment.
`KO_abundance` `metadata`	The KOs abundance table and group table.
`KO_enrich()` `as.enrich_res()`	Perform enrichment analysis
`KO_fisher()`	Perform fisher's exact enrichment analysis
`KO_gsa()`	Perform gene set analysis
`KO_gsea()`	Perform gene set enrichment analysis
`KO_gsva()`	Perform Gene Set Variation Analysis
`KO_htable`	KO htable from 'KEGG'
`KO_padog()`	Perform Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
`KO_safe()`	Perform Significance Analysis of Function and Expression
`KO_sea()`	Perform Simultaneous Enrichment Analysis
`KOlist`	The KOlist used for enrichment.
`Module_htable`	Module htable from 'KEGG'
`Pathway_htable`	Pathway htable from 'KEGG'
`RSA_by_cm()` `extract_cluster()` `plot_c_means()`	Reporter score analysis after C-means clustering
`cm_test_k()` `c_means()`	Test the proper clusters k for c_means
`combine_rs_res()`	Combine the results of 'step by step GRSA'
`custom_modulelist()` `transform_modulelist()`	Build a custom modulelist
`custom_modulelist_from_org()`	Custom modulelist from a specific organism
`gene2ko()`	Transfer gene symbol table to KO table
`genedf`	human gene table
`get_features()`	get features in a modulelist
`get_reporter_score()`	Calculate reporter score
`hsa_kegg_pathway`	pathway information for "hsa"
`ko.test()`	Differential analysis or Correlation analysis for KO-abundance table
`load_CARDinfo()`	Load the CARDinfo (from CARD database)
`load_GOlist()` `load_GOinfo()`	Load the GOlist (from 'GO' database)
`load_htable()` `load_KOlist()` `load_CPDlist()` `load_KO_desc()` `load_KO_htable()` `load_Pathway_htable()` `load_Module_htable()` `load_Compound_htable()` `load_org_pathway()`	Load the specific table (from 'KEGG')
`mmu_kegg_pathway`	pathway information for "mmu"
`modify_description()`	Modify the pathway description before plotting
`plot(<cm_res>)`	Plot c_means result
`plot_KEGG_map()`	plot_KEGG_map
`plot_enrich_res()` `plot(<enrich_res>)`	Plot enrich_res
`plot_features_box()`	Plot features boxplot
`plot_features_distribution()`	plot the Z-score of features distribution
`plot_features_heatmap()`	Plot features heatmap
`plot_features_in_pathway()`	Plot features trend in one pathway or module
`plot_features_network()`	Plot features network
`plot_htable()`	Plot htable levels
`plot_report()`	Plot the reporter_res
`plot_report_circle_packing()`	Plot the reporter_res as circle_packing
`plot_significance()`	Plot the significance of pathway
`print(<reporter_score>)`	Print reporter_score
`print(<rs_by_cm>)`	Print rs_by_cm
`pvalue2zs()`	Transfer p-value of KOs to Z-score
`reporter_score()`	One step to get the reporter score of your KO abundance table.
`reporter_score_res` `reporter_score_res2`	`reporter_score()` result from KO_abundance_test
`up_level_KO()`	Upgrade the KO level
`update_CARDinfo()`	update CARDinfo from (from 'CARD' database)
`update_GOlist()` `update_GOinfo()`	Update the GO2gene files (from 'GO' database)
`update_KEGG()` `update_KO_file()` `update_htable()` `update_org_pathway()`	Update files from 'KEGG'

Reference

All functions