Package index • MetaProViz

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(): —————————

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(): —————————

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