hmdb_table: Download a HMDB XML file and process it into a table

In saezlab/OmnipathR: OmniPath web service client and more

Download a HMDB XML file and process it into a table

Description

Download a HMDB XML file and process it into a table

Usage

hmdb_table(dataset = "metabolites", fields = NULL)

Arguments

dataset

Character: name of an HMDB XML dataset, such as "metabolites", "proteins", "urine", "serum", "csf", "saliva", "feces", "sweat".

fields

Character: fields to extract from the XML. This is a very minimal parser that is able to extract the text content of simple fields and multiple value fields which contain a list of leaves within one container tag under the record tag. A full list of fields available in HMDB is available by the hmdb_protein_fields and hmdb_metabolite_fields functions. By default, all fields available in the dataset are extracted.

Value

A data frame (tibble) with each column corresponding to a field.

See Also

• hmdb_protein_fields

• hmdb_metabolite_fields

Examples

hmdb_table()

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.