map_to_kegg_webchem: #' Convert metabolite name table to KEGG metabolite table #'...

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

#' Convert metabolite name table to KEGG metabolite table #' #' @importFrom MetaboAnalystR InitDataObjects #' @importFrom MetaboAnalystR Setup.MapData #' @importFrom MetaboAnalystR CrossReferencing #' @importFrom MetaboAnalystR CreateMappingResultTable #' @import data.table #' @param met_table Table of metabolite abundances #' @return A new table of metabolite abundances using KEGG compound IDs #' @examples #' new_mets = map_to_kegg(mets) #' @export map_to_kegg = function(met_table) mSet = InitDataObjects("NA", "utils", FALSE) cmpds = met_table[,compound] mSet = Setup.MapData(mSet, cmpds) mSet = CrossReferencing(mSet, "name", kegg = T) mSet = CreateMappingResultTable(mSet) match_table = data.table(mSet$dataSet$map.table) num_nas = nrow(match_table[is.na(KEGG)|KEGG=="NA"]) if(num_nas > 0) warning(paste0(num_nas, " metabolites were not matched to KEGG IDs and will be ignored")) met_table = merge(met_table, match_table[,list(Query, KEGG)], by.x = "compound", by.y = "Query", all.x = T)[!is.na(KEGG) & KEGG != "NA"] met_table = met_table[,lapply(.SD, sum), by=KEGG, .SDcols = names(met_table)[!names(met_table) setnames(met_table, "KEGG", "compound") return(met_table) Convert metabolite name table to KEGG metabolite table, using webchem package (fewer installation issues than MetaboAnalystR)

Description

#' Convert metabolite name table to KEGG metabolite table #' #' @importFrom MetaboAnalystR InitDataObjects #' @importFrom MetaboAnalystR Setup.MapData #' @importFrom MetaboAnalystR CrossReferencing #' @importFrom MetaboAnalystR CreateMappingResultTable #' @import data.table #' @param met_table Table of metabolite abundances #' @return A new table of metabolite abundances using KEGG compound IDs #' @examples #' new_mets = map_to_kegg(mets) #' @export map_to_kegg = function(met_table) mSet = InitDataObjects("NA", "utils", FALSE) cmpds = met_table[,compound] mSet = Setup.MapData(mSet, cmpds) mSet = CrossReferencing(mSet, "name", kegg = T) mSet = CreateMappingResultTable(mSet) match_table = data.table(mSet$dataSet$map.table) num_nas = nrow(match_table[is.na(KEGG)|KEGG=="NA"]) if(num_nas > 0) warning(paste0(num_nas, " metabolites were not matched to KEGG IDs and will be ignored")) met_table = merge(met_table, match_table[,list(Query, KEGG)], by.x = "compound", by.y = "Query", all.x = T)[!is.na(KEGG) & KEGG != "NA"] met_table = met_table[,lapply(.SD, sum), by=KEGG, .SDcols = names(met_table)[!names(met_table) setnames(met_table, "KEGG", "compound") return(met_table) Convert metabolite name table to KEGG metabolite table, using webchem package (fewer installation issues than MetaboAnalystR)

Usage

map_to_kegg_webchem(met_table)

Arguments

met_table

Table of metabolite abundances

Value

A new table of metabolite abundances using KEGG compound IDs

Examples

new_mets = map_to_kegg_webchem(mets)

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.