# Generalized Reporter Score-Based Enrichment Analysis for Omics Data

## Documentation for package ‘ReporterScore’ version 0.2.5

- 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
c_net_from_pathway_xml | Create a network from KEGG pathway XML files
download_org_pathway | Update files from 'KEGG'
export_report_table | Export report score result tables
extract_cluster | Reporter score analysis after C-means clustering
gene2ko | Transfer gene symbol table to KO table
genedf | human gene table
get_all_pathway_net_index | Create an index for all KEGG pathway networks
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_CAZy_info | Load the CAZy_info (from CAZy database)
load_Compound_htable | Load the specific table (from 'KEGG')
load_CPDlist | Load the specific table (from 'KEGG')
load_Enzyme_htable | Load the specific table (from 'KEGG')
load_Enzyme_info | Load the Enzyme_info (from ExPASy Enzyme database)
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')
load_pathway_xml_ls | Load KEGG pathway XML file list
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'
parse_enzyme_dat | Parse enzyme.dat file into a structured data frame
Pathway_htable | Pathway htable from 'KEGG'
pathway_net_index | Create a pathway network index data.frame
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_pathway_net | Plot a KEGG pathway 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_CAZy_info | Update CAZy_info from CAZy database
update_Enzyme_info | Update Enzyme_info from ExPASy Enzyme 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'
update_pathway_xml_ls | Download KEGG pathway XML files and create networks
up_level_KO | Upgrade the KO level