# METabolomics pre-PRocessing, functiOnal analysis and VIZualisation

## Documentation for package ‘MetaProViz’ version 4.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

MetaProViz-package | The MetaProViz package
alanine_pathways | alanine_pathways
biocrates_features | biocrates_features
cellular_meta | cellular_meta
checkmatch_pk_to_data | Check and summarize relationship between prixor knowledge to measured
cluster_ora | Overrepresentation analysis by cluster
cluster_pk | Cluster terms in prior knowledge by set overlap
compare_pk | Compare Prior Knowledge Resources and/or Columns within a Single Resource
count_id | Count Entries and Generate a Histogram Plot for a Specified Column
dma | Differential metabolite analysis
equivalent_features | equivalent_features
equivalent_id | Find additional potential IDs for "kegg", "pubchem", "chebi", "hmdb"
gaude_pathways | gaude_pathways
get_exclusion_metabolites | Metabolites excluded from prior knowledge resources
hallmarks | hallmarks
intracell_dma | intracell_dma
intracell_raw | intracell_raw
intracell_raw_se | intracell_raw_se
make_gene_metab_set | Create metabolite sets from existing genesets
mapping_ambiguity | Create Mapping Ambiguities between two ID types
mca_2cond | Metabolite clustering analysis for two conditions
mca_core | Metabolite clustering analysis for core experiments
mca_core_rules | mca_core_rules
mca_twocond_rules | mca_twocond_rules
medium_raw | medium_raw
metadata_analysis | PCA-based metadata analysis
MetaProViz | The MetaProViz package
metaproviz_config_path | Current config file path of MetaProViz
metaproviz_load_config | Load the package configuration from a config file
metaproviz_log | Browse the current MetaProViz log file
metaproviz_logfile | Path to the current MetaProViz log file
metaproviz_reset_config | Restore the built-in default values of all config parameters of MetaProViz
metaproviz_save_config | Save the current package configuration
metaproviz_set_loglevel | Sets the log level for the package logger
meta_pk | Meta prior-knowledge
metsigdb_chemicalclass | Metabolite chemical classes from RaMP DB
metsigdb_kegg | KEGG pathways
metsigdb_macdb | Retrieve MACDB metabolite-cancer associations.
metsigdb_metalinks | Annotated metabolite-protein interactions from MetalinksDB
metsigdb_reactome | Retrieve Reactome metabolite sets suitable for ORA.
metsigdb_wikipathways | Retrieve WikiPathways metabolite mapping suitable for ORA.
pool_estimation | Find metabolites with high variability across total pool samples
processing | Data preprocessing and normalization
replicate_sum | Merges the analytical replicates of an experiment
standard_ora | Overrepresentation analysis of metabolite sets in pathways
tissue_dma | tissue_dma
tissue_dma_old | tissue_dma_old
tissue_dma_young | tissue_dma_young
tissue_meta | Tissue_Metadata
tissue_norm | tissue_norm
tissue_norm_se | tissue_norm_se
tissue_tvn_proteomics | tissue_tvn_proteomics
tissue_tvn_rnaseq | tissue_tvn_rnaseq
translate_id | Translate IDs to/from KEGG, PubChem, Chebi, HMDB
traverse_ids | Expand metabolite IDs by traversing RaMP ID mappings
viz_graph | Graph visualization for clustered terms
viz_heatmap | Heatmap visualization
viz_pca | This script allows you to perform PCA plot visualization using the results of the MetaProViz analysis
viz_superplot | This script allows you to perform different visualizations (bar, box, violin plots) using the results of the MetaProViz analysis
viz_volcano | Volcano plot