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RAMP_hmdb: A list containing network plot information about pathways from the SMPDB database

Source: R/Cleaned_Reference_Metabolite_Databases.R
RAMP_hmdb.Rd

This object contains a collection of information for each graphite SMPDB network, including their source, destination, direction, and reaction type for both proteins and metabolites. Topology sources were retrieved on 2022-11-01; node identifiers were re-harmonised and integrity-checked against the bundled RaMP-DB 3.0.7 snapshot.

Usage

RAMP_hmdb

Format

A list with 10 elements:

id

SMPDB pathway identifier (character)

title

Pathway title (character)

database

Source database (character)

species

Species (character)

protEdges

Protein interactions: a data frame with src, dest, directed, reaction_type, and source_reaction_type. Row counts vary by pathway.

protPropEdges

Propagated protein interactions: a data frame with src, dest, directed, reaction_type, and source_reaction_type. Row counts vary by pathway.

metabolEdges

Metabolite interactions: a data frame with src, dest, directed, reaction_type, and source_reaction_type. Row counts vary by pathway.

metabolPropEdges

Propagated metabolite interactions: a data frame with src, dest, directed, reaction_type, and source_reaction_type. Row counts vary by pathway.

mixedEdges

Protein-metabolite interactions: a data frame with src, dest, directed, reaction_type, and source_reaction_type. Row counts vary by pathway.

timestamp

The date of data extraction (Date)

Details

Interaction labels and directions were restored from the pinned graphite archive. Edge tables retain the exact label in source_reaction_type; spamtp_interaction_repair records the repair provenance on the collection. See vignette("Pathway_Database_Integration", package = "SpaMTP").