chemicalClassSurveyRampIdsFullPopConn: chemicalClassSurveyRampIdsFullPopConn2 is a helper function...

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

chemicalClassSurveyRampIdsFullPopConn2 is a helper function that takes a list of metabolite ids and a MariaDB Connection object and returns metabolite class information for the metabolite list and a population of all ramp metabolites.

Description

chemicalClassSurveyRampIdsFullPopConn2 is a helper function that takes a list of metabolite ids and a MariaDB Connection object and returns metabolite class information for the metabolite list and a population of all ramp metabolites.

Usage

chemicalClassSurveyRampIdsFullPopConn(db = RaMP(), mets, inferIdMapping = TRUE)

Arguments

mets	a list object of prefixed metabolite ids of interest
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 April 28, 2024, 3:28 a.m.