Workflows: panoply_metaboanalyst_workflow

panoply_metaboanalyst_workflow

Description

This workflow executes a PANOPLY adaptation of MetaboAnalyst, performing pathway enrichment of metabolomic (and proteomic/transcriptomic) features and generates an interactive report. The workflow is based off the 6.0 release of MetaboAnalyst; all databases are pulled from that version (Pang, Z. et al. 2024). It executes the following modules:

module	description
panoply_metaboanalyst	performs joint-pathway enrichment analysis on metabolites and an additional -ome
panoply_metaboanalyst_report	creates an interactive R Markdown report of the pathway-analysis results

Input

Required inputs:

• meta_gct: (.gct file) normalized metabolomic data table in the form of a GCT

• omic_gct: (.gct file) normalized -omic data table in the form of a GCT (optional but recommended)

• ome_type: (String) type of -omic data provided, e.g. "RNA" or "proteome" (optional but recommended)

• groups_file: (.csv file) annotation file, subsetted to annotations of interest for this analysis (optional but recommended)

• output_prefix: (String) prefix used to name the results files

• yaml_file: (.yaml file) master-parameters.yaml

Optional inputs:

panoply_metaboanalyst

• anal_type: (String, default="ORA") type of pathway-enrichment analysis to be performed ("ORA" for Overrepresentation Analysis or "QEA" for Quantitative Enrichment Analysis); ORA is recommended for joint-pathway analysis

• pval_comb: (String, default="pvalo") method for combining p-values in multiomic enrichment analysis; options include "query" (combine queries), "pvalu" (unweighted), "pvalo" (overall), or "pvalp" (pathway-level)

• max_annot_levels: (Int, default=10) max number of levels in an annotation category, to be considered qualitative and included in the analysis

• pval_signif: (Float, default=0.05) p-value threshold for significant enrichement

• top_n_networks: (Int, default=10) top N networks to plot per annot subvalue

• meta_id_col: (String, default="metab_ids") rdesc column in Metabolite GCT with meta_id_type IDs; if set to NULL, GCT rid values will be used.

• meta_id_type: (String, default="hmdb_id") ID type used for metabolites

• gene_column: (String, default="geneSymbol") rdesc column in -omic GCT with gene IDs

• gene_id_type: (String, default="SYMBOL") ID type used for gene IDs

Output

panoply_metaboanalyst_workflow produces the follow outputs:

• metaboanalyst_tar: (.tar) An output tar file that contains the metaboanalyst analysis results
• metaboanalyst_report: (.html file) Interactive R Markown report.

References

1. Pang, Z. et al. MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation. Nucleic Acids Research 52, W398–W406 (2024).