Package index • MetaProViz

All functions

AddInfo(): Adds extra columns to enrichment output that inform about 1. The amount of genes associated with term in prior knowledge, 2. The amount of genes detected in input data associated with term in prior knowledge, and 3. The percentage of genes detected in input data associated with term in prior knowledge.

CleanMapping(): Reduce mapping ambiguities by using detected IDs

ClusterORA(): —————————

ClusterPK(): Deal with detected input features. If we only have one ID, could it also be another one?

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

DetectedID(): Clean translated ID in prior knowledge based on measured features

LoadHallmarks(): Toy Data Import

LoadKEGG(): KEGG

LoadMetalinks(): Function to

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_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

PossibleID(): Deal with detected input features.

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