cts_convert: Convert Ids using Chemical Translation Service (CTS)

Description Usage Arguments Details Value Note References See Also Examples

View source: R/cts.R

Description

Convert Ids using Chemical Translation Service (CTS), see http://cts.fiehnlab.ucdavis.edu/

Usage

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cts_convert(
  query,
  from,
  to,
  match = c("all", "first", "ask", "na"),
  verbose = getOption("verbose"),
  choices = NULL,
  ...
)

Arguments

query

character; query ID.

from

character; type of query ID, e.g. 'Chemical Name' , 'InChIKey', 'PubChem CID', 'ChemSpider', 'CAS'.

to

character; type to convert to.

match

character; How should multiple hits be handled? "all" returns all matches, "first" returns only the first result, "ask" enters an interactive mode and the user is asked for input, "na" returns NA if multiple hits are found.

verbose

logical; should a verbose output be printed on the console?

choices

deprecated. Use the match argument instead.

...

currently not used.

Details

See also http://cts.fiehnlab.ucdavis.edu/ for possible values of from and to.

Value

a list of character vectors or if choices is used, then a single named vector.

Note

When this version of webchem was released, CTS was temporarily unable to convert chemical names to IDs.

References

Wohlgemuth, G., P. K. Haldiya, E. Willighagen, T. Kind, and O. Fiehn 2010The Chemical Translation Service – a Web-Based Tool to Improve Standardization of Metabolomic Reports. Bioinformatics 26(20): 2647–2648.

See Also

cts_from for possible values in the 'from' argument and cts_to for possible values in the 'to' argument.

Examples

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# might fail if API is not available
cts_convert("XEFQLINVKFYRCS-UHFFFAOYSA-N", "inchikey", "Chemical Name")

### multiple inputs
keys <- c("XEFQLINVKFYRCS-UHFFFAOYSA-N", "VLKZOEOYAKHREP-UHFFFAOYSA-N")
cts_convert(keys, "inchikey", "cas")

webchem documentation built on Dec. 11, 2021, 9:54 a.m.