SearchKEGG: Function to find a compound information using his id by...

In cherkaos/MetabToPathways: Query metabolites to find their pathways, for multiple databases (Kegg, SMPDB, HMDB and Biocyc)

Usage

SearchKEGG(id, type)

Arguments

id
type

Author(s)

Sarah Cherkaoui

References

1. 4Creek DJ, Jankevics A, Burgess KE, Breitling R, Barrett MP. IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data. Bioinformatics. 2012 Apr 1;28(7):1048-9.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (id, type) 
{
    position <- vector()
    if (type == "name") {
        position <- Mmatch(id, DBKEGG[, 3])
    }
    if (type == "pubchem") {
        position <- Mmatch(id, DBKEGG[, 9])
    }
    if (type == "hmdb") {
        position <- Mmatch(id, DBKEGG[, 11])
    }
    if (type == "kegg") {
        position <- Mmatch(id, DB1DBKEGG[, 8])
    }
    if (type == "biocyc") {
        position <- Mmatch(id, DBKEGG[, 12])
    }
    if (type == "inchikey") {
        position <- Mmatch(id, DBKEGG[, 15])
    }
    if (length(position) > 0) {
        Name <- fixlc(DBKEGG[position, 3])
        Pubchem <- fixlc(DBKEGG[position, 9])
        HMDB <- fixlc(DBKEGG[position, 11])
        KeggID <- fixlc(DBKEGG[position, 8])
        BioCyc <- fixlc(DBKEGG[position, 12])
        InchiKey <- fixlc(DBKEGG[position, 15])
        Map <- fixlc(DBKEGG[position, 5])
        KeggPathway <- fixlc(strsplit(DBKEGG[position, 6], "__"))
        KeggPathID <- fixlc(DBSMPDB[position, 7])
        return(list(Name = Name, Pubchem = Pubchem, HMDB = HMDB, 
            KeggID = KeggID, BioCyc = BioCyc, InchiKey = InchiKey, 
            Map = Map, KeggPathway = KeggPathway, KeggPathID = KeggPathID))
    }
    else (return("error"))
  }

cherkaos/MetabToPathways documentation built on May 13, 2019, 3:54 p.m.