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I am attempting to use your hmdbQuery R package to pull metadata for a list of metabolites from hmdb. I am able to do this for about 215/366 metabolites. At this point, I am most interested in taxonomy.
The most common error I am getting is:
"Error in if (tissues[1] == "\n ") tissues = NULL : argument is of length zero"
from the following query:
Also, what is the role of secondary accession numbers? Do these always point to the same record? Is there ever a case where a secondary number might work with the package but the primary doesn't?
I am attempting to use your hmdbQuery R package to pull metadata for a list of metabolites from hmdb. I am able to do this for about 215/366 metabolites. At this point, I am most interested in taxonomy.
The most common error I am getting is:
"Error in if (tissues[1] == "\n ") tissues = NULL : argument is of length zero"
from the following query:
hmdb_result = HmdbEntry(
prefix = "http://www.hmdb.ca/metabolites/",
id = "HMDB0002467",
keepFull = TRUE
)
Thank you! Aaron
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