IonIdentityMolecularNetworking Class Reference

#include <OpenMS/ANALYSIS/ID/IonIdentityMolecularNetworking.h>

Static Public Member Functions

static void annotateConsensusMap (ConsensusMap &consensus_map)
static void writeSupplementaryPairTable (const ConsensusMap &consensus_map, const String &output_file)

Member Function Documentation

◆ annotateConsensusMap()

static void annotateConsensusMap ( ConsensusMap consensus_map)

Annotate ConsensusMap for ion identity molecular networking (IIMN) workflow by GNPS. Adds meta values Constants::UserParams::IIMN_ROW_ID (unique index for each feature), Constants::UserParams::IIMN_ADDUCT_PARTNERS (related features row IDs) and Constants::UserParams::IIMN_ANNOTATION_NETWORK_NUMBER (all related features with different adduct states) get the same network number). This method requires the features annotated with the Constants::UserParams::IIMN_LINKED_GROUPS meta value. If at least one of the features has an annotation for Constants::UserParam::IIMN_LINKED_GROUPS, annotate ConsensusMap for IIMN.

Referenced by TOPPGNPSExport::main_().

◆ writeSupplementaryPairTable()

static void writeSupplementaryPairTable ( const ConsensusMap consensus_map,
const String output_file 

Write supplementary pair table (csv file) from a consensusXML file with edge annotations for connected features. Required for GNPS IIMN. The table contains the columns "ID 1" (row ID of first feature), "ID 2" (row ID of second feature), "EdgeType" (MS1/2 annotation), "Score" (the number of direct partners from both connected features) and "Annotation" (adducts and delta m/z between two connected features).

Referenced by TOPPGNPSExport::main_().