Package index • MetaProViz

All functions

ClusterORA(): —————————

ClusterORA

DMA(): This function allows you to perform differential metabolite analysis to obtain a Log2FC, pval, padj and tval comparing two or multiple conditions.

EquivalentIDs(): Find additional potential IDs for "kegg", "pubchem", "chebi", "hmdb"

LoadGaude(): Prior Knowledge Import

LoadHallmarks(): Prior Knowledge Import

LoadKEGG(): KEGG

LoadMetalinks(): Function to

LoadRAMP(): Prior Knowledge Import

MCA_2Cond(): —————————

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_rules(): MCA regulatory rules Import

Make_GeneMetabSet(): Function to add metabolite HMDB IDs to existing genesets based on cosmosR prior knowledge

MappingAmbiguity(): Create Mapping Ambiguities between two ID types

MetaAnalysis(): 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.

MetaPK(): Meta prior-knowledge

MetaProViz-package MetaProViz: The MetaProViz package

MetaProViz_log(): Browse the current MetaProViz log file

MetaProViz_logfile(): Path to the current MetaProViz log file

MetaProViz_set_loglevel(): Sets the log level for the package logger

PoolEstimation(): Find metabolites with high variability across total pool samples

PreProcessing(): Modularised Normalization: 80%-filtering rule, total-ion count normalization, missing value imputation and Outlier Detection: HotellingT2.

ReplicateSum(): Merges the analytical replicates of an experiment

StandardORA(): Uses enricher to run ORA on the differential metabolites (DM) using a pathway list

ToyData(): Access built-in example data

TranslateID(): Translate IDs to/from KEGG, PubChem, Chebi, HMDB

VizHeatmap(): Heatmap visualization

VizPCA(): This script allows you to perform PCA plot visualization using the results of the MetaProViz analysis PCA plot visualization

VizSuperplot(): 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

VizVolcano(): This script allows you to perform different data visualizations using the results of the MetaProViz analysis Volcano plot visualization

metaproviz_config_path(): Current config file path of MetaProViz

metaproviz_load_config(): Load the package configuration from a config file

metaproviz_reset_config(): Restore the built-in default values of all config parameters of MetaProViz

metaproviz_save_config(): Save the current package configuration