HMDB_ID_from_ID: Query Human Metabolome Database by metabolite name

In venkmurthy/vmtools: Venk Murthy's Handy Tools

Query Human Metabolome Database by metabolite name

Description

This function searches the HMDB to find the canonical HMDB ID for a given ID.

Usage

HMDB_ID_from_ID(ids, max.tries = 5)

Arguments

max.tries	number of times to retry loading a page
id	vector of strings with ID starting with "HMDB" or numbers with just the numeric part

Value

vector of strings with canonical HMDB IDs

Examples

HMDB_ID_from_ID(22)
HMDB_ID_from_ID("HMDB0006022")
HMDB_ID_from_ID("HMDB1162")

id.list <- c("Internal Standard","Internal Standard","HMDB00123","HMDB00161","HMDB00187","HMDB00167",
            "HMDB00696","HMDB00148","HMDB00168","HMDB00641","HMDB00177","HMDB00517",
            "HMDB00182","HMDB00883","HMDB00687","HMDB00172","HMDB00159","HMDB00158",
            "HMDB00929","HMDB00162","HMDB00725","HMDB00214","HMDB00904","HMDB00251",
            "HMDB00112","HMDB00092","HMDB01539","HMDB03334","HMDB29416","HMDB01906*",
            "HMDB00715","HMDB00898","HMDB00026","HMDB00235","HMDB01406","HMDB00043",
            "HMDB00097","HMDB00086","HMDB00895","HMDB00064","HMDB00562","HMDB00248",
            "HMDB00925","HMDB00050","HMDB00630","HMDB00299","HMDB01046","HMDB00716",
            "HMDB00699","HMDB01161","HMDB02005","HMDB00062","HMDB00201","HMDB00824",
            "HMDB13133","HMDB02013","HMDB13127","HMDB00688","HMDB02366","HMDB13130",
            "HMDB00705","HMDB13238","HMDB00791","HMDB13288","HMDB00651","HMDB13325",
            "HMDB02250","HMDB13326","HMDB05066","HMDB02014","HMDB13331","HMDB00222",
            "HMDB00848","HMDB05065","HMDB06469","HMDB06347","HMDB11103","HMDB03331",
            "HMDB01563","HMDB04030","HMDB00991*","HMDB32390","HMDB05862",NA,
            "HMDB00479","HMDB03681","HMDB01867","HMDB03464","HMDB13678","HMDB04400",
            "HMDB00982","HMDB01182","HMDB00897","HMDB01859","HMDB00212","HMDB60994",
            "HMDB01008","HMDB01847","HMDB1162","HMDB00063","HMDB02802","HMDB31404")

t0 <- Sys.time()
HMDB_ID_from_ID(id.list)
Sys.time() -t0

venkmurthy/vmtools documentation built on Oct. 16, 2024, 10:48 a.m.