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All functions

MetaProViz-package MetaProViz
The MetaProViz package
alanine_pathways
alanine_pathways
biocrates_features
biocrates_features
cellular_meta
cellular_meta
checkmatch_pk_to_data()
Check and summarize prior_knowledge-to-MeasuredFeatures relationship
cluster_ora()

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cluster_ora

compare_pk()
Compare Prior Knowledge Resources and/or Columns within a Single Resource and Generate an UpSet Plot
count_id()
Count Entries and Generate a Histogram Plot for a Specified Column
dma()
This function allows you to perform differential metabolite analysis to obtain a Log2FC, pval, padj and tval comparing two or multiple conditions.
equivalent_features
equivalent_features
equivalent_id()
Find additional potential IDs for "kegg", "pubchem", "chebi", "hmdb"
gaude_pathways
gaude_pathways
hallmarks
hallmarks
intracell_dma
intracell_dma
intracell_raw
intracell_raw
make_gene_metab_set()
Function to add metabolite HMDB IDs to existing genesets based on cosmosR prior knowledge
mapping_ambiguity()
Create Mapping Ambiguities between two ID types
mca_2cond()

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This script performs metabolite clustering analysis and computes clusters of metabolites based on regulatory rules between conditions.

mca_core()
This script performs metabolite clustering analysis and computes clusters of metabolites based on regulatory rules between Intracellular and culture media metabolomics (core experiment).
mca_core_rules
mca_core_rules
mca_twocond_rules
mca_twocond_rules
medium_raw
medium_raw
meta_pk()
Meta prior-knowledge
metadata_analysis()
This function performs a PCA analysis on the input data and combines it with the sample metadata to perform an ANOVA test to identify significant differences between the groups.
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
metsigdb_chemicalclass()
Prior Knowledge Import
metsigdb_kegg()
KEGG
metsigdb_metalinks()
Annotated metabolite-protein interactions from MetalinksDB
pool_estimation()
Find metabolites with high variability across total pool samples
processing()
Modularised Normalization: 80%-filtering rule, total-ion count normalization, missing value imputation and Outlier Detection: HotellingT2.
replicate_sum()
Merges the analytical replicates of an experiment
standard_ora()
Uses enricher to run ORA on the differential metabolites (DM) using a pathway list
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_tvn_proteomics
tissue_tvn_proteomics
tissue_tvn_rnaseq
tissue_tvn_rnaseq
translate_id()
Translate IDs to/from KEGG, PubChem, Chebi, HMDB
viz_heatmap()
Heatmap visualization
viz_pca()
This script allows you to perform PCA plot visualization using the results of the MetaProViz analysis PCA plot visualization
viz_superplot()
This script allows you to perform different visualizations (bar, box, violin plots) using the results of the MetaProViz analysis Bar, Box or Violin plot in Superplot style visualization
viz_volcano()
This script allows you to perform different data visualizations using the results of the MetaProViz analysis Volcano plot visualization