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isglobal-brge / brgeEnrich

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Specifying variables #1

Open MathieuUm opened 1 month ago

MathieuUm commented 1 month ago

Hello, I'm trying to create an automatic workflow to process map data using your API which queries the CPDB. I wanted to know if there was a way to specify the minimum number of metabolites present in a pathway for it to come out and, if it was possible to choose the database(s) one wishes to use. Thanks in advance for your feedback. Sincerely, MU

dpelegri commented 1 month ago

Hi MU,

Thanks for using brgeEnrich,

The API implemented in this package is a very simple api with the basic CPDB utilities. At this time you cannot specify the minimum amount of metabolites present in a pathway, it simply performs the complete query to CPDB and returns the results. Regarding the database, there is a parameter in some functions, 'accType', to set the database where specified codes belongs to. For metabolites the possible values ​​would be,

# Accession number types for metabolites
getCpdbAccessionTypes('metabolites')

 [1] "chebi" "hmdb" "kegg"
 [4] "chembl" "pubchem-compound" "pubchem-substance"
 [7] "cas" "drugbank"

Best,