chemicalClassSurveyRampIdsConn: chemicalClassSurveyRampIdsConn2 is a helper function that...

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

chemicalClassSurveyRampIdsConn2 is a helper function that takes a list of metabolite ids, a list of 'population' metabolite ids and a MariaDB Connection object. The method returns metabolite class information for the metabolite list and a population of all ramp metabolites.

Description

chemicalClassSurveyRampIdsConn2 is a helper function that takes a list of metabolite ids, a list of 'population' metabolite ids and a MariaDB Connection object. The method returns metabolite class information for the metabolite list and a population of all ramp metabolites.

Usage

chemicalClassSurveyRampIdsConn(mets, pop, conn, inferIdMapping = TRUE)

Arguments

mets	a list object of prefixed metabolite ids of interest
pop	a list object of prefixed metabolite ids, representing a larger population of metabolites from which the mets were selected.
conn	a MariaDB Connection object to support queries
inferIdMapping	if FALSE, the survey only reports on class annotations made directly on the input ids. If inferIdMapping is set to TRUE, the ids are cross-referenced or mapped to related ids that contain metabolite class annotations. The default is TRUE.

Value

a list object containing three objects 'count_summary', 'met_classes' and 'met_query_report'. The count_summary is a dataframe containing metabolite classes and number of metabolites in each class. The met_classes is a detailed listing of compound classes associated with each input metabolite The met_query_report indicates the number of input metabolites, how many were found in the DB and the list of metabolites not found in RaMP DB.

ncats/RaMP-DB documentation built on Oct. 28, 2023, 8:12 a.m.