SearchHMDB:

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

Usage

SearchHMDB(hmdb, info = "Pathways")

Arguments

hmdb
info

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 (hmdb, info = "Pathways") 
{
    switch(info, Pathways = "pathway/name", Biocyc = "biocyc_id", 
        Synonyms = "synonym", CellularLocation = "cellular_location", 
        BiofluidLocation = "biofluid", TissueLocation = "tissue")
    if (!hmdb == "error" || !is.null(hmdb)) {
        url <- paste0("http://www.hmdb.ca/metabolites/", hmdb, 
            ".xml")
        xmlhttp <- getURL(url)
        if (grepl("metabolite", xmlhttp, ignore.case = TRUE) == 
            TRUE) {
            if (is.null(xmlhttp)) {
                return("error")
            }
            else {
                doc <- (xmlParse(xmlhttp))
                src <- tryCatch(xpathSApply(doc, paste0("//", 
                  info), xmlValue), error = function(e) {
                  NULL
                })
                if (length(src) > 0) {
                  src <- unlist(src)
                  return(src)
                }
                else (return("error"))
            }
        }
        else {
            return("error")
        }
    }
    else {
        return("error")
    }
  }

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