Generalized Reporter Score-Based Enrichment Analysis for Omics Data

---

Documentation for package ‘ReporterScore’ version 0.1.6

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

Help Pages

as.enrich_res	Perform enrichment analysis
cm_test_k	Test the proper clusters k for c_means
combine_rs_res	Combine the results of 'step by step GRSA'
Compound_htable	Compound htable from 'KEGG'
CPDlist	The CPDlist used for enrichment.
custom_modulelist	Build a custom modulelist
custom_modulelist_from_org	Custom modulelist from a specific organism
c_means	Test the proper clusters k for c_means
download_org_pathway	Update files from 'KEGG'
extract_cluster	Reporter score analysis after C-means clustering
gene2ko	Transfer gene symbol table to KO table
genedf	human gene table
get_features	get features in a modulelist
get_KOs	get features in a modulelist
get_org_pathway	Update files from 'KEGG'
get_reporter_score	Calculate reporter score
GOlist	The GOlist used for enrichment.
GRSA	One step to get the reporter score of your KO abundance table.
GRSA_by_cm	Reporter score analysis after C-means clustering
hsa_kegg_pathway	pathway information for "hsa"
ko.test	Differential analysis or Correlation analysis for KO-abundance table
KOlist	The KOlist used for enrichment.
KO_abundance	The KOs abundance table and group table.
KO_enrich	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
load_CARDinfo	Load the CARDinfo (from CARD database)
load_Compound_htable	Load the specific table (from 'KEGG')
load_CPDlist	Load the specific table (from 'KEGG')
load_GOinfo	Load the GOlist (from 'GO' database)
load_GOlist	Load the GOlist (from 'GO' database)
load_htable	Load the specific table (from 'KEGG')
load_KOlist	Load the specific table (from 'KEGG')
load_KO_desc	Load the specific table (from 'KEGG')
load_KO_htable	Load the specific table (from 'KEGG')
load_Module_htable	Load the specific table (from 'KEGG')
load_org_pathway	Load the specific table (from 'KEGG')
load_Pathway_htable	Load the specific table (from 'KEGG')
metadata	The KOs abundance table and group table.
mmu_kegg_pathway	pathway information for "mmu"
modify_description	Modify the pathway description before plotting
Module_htable	Module htable from 'KEGG'
Pathway_htable	Pathway htable from 'KEGG'
plot.cm_res	Plot c_means result
plot.enrich_res	Plot enrich_res
plot_c_means	Reporter score analysis after C-means clustering
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_KEGG_map	plot_KEGG_map
plot_KOs_box	Plot features boxplot
plot_KOs_distribution	plot the Z-score of features distribution
plot_KOs_heatmap	Plot features heatmap
plot_KOs_in_pathway	Plot features trend in one pathway or module
plot_KOs_network	Plot features network
plot_report	Plot the reporter_res
plot_report_bar	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()' result from KO_abundance_test
reporter_score_res2	'reporter_score()' result from KO_abundance_test
RSA	One step to get the reporter score of your KO abundance table.
RSA_by_cm	Reporter score analysis after C-means clustering
transform_modulelist	Build a custom modulelist
update_CARDinfo	update CARDinfo from (from 'CARD' database)
update_GOinfo	Update the GO2gene files (from 'GO' database)
update_GOlist	Update the GO2gene files (from 'GO' database)
update_htable	Update files from 'KEGG'
update_KEGG	Update files from 'KEGG'
update_KO_file	Update files from 'KEGG'
update_org_pathway	Update files from 'KEGG'
up_level_KO	Upgrade the KO level