Fetch and parse the 'psi-ms.obo' and some metadata from the usual sources to use as ontology.
Source:R/obo.R
getCVDictionary.Rd
If use_local_fallback
is TRUE, this function will never fail. Otherwise, it may fail if the internet connection
is flawed or internal URLs related to GitHubs API become stale.
Usage
getCVDictionary(
source = c("latest", "local", "custom"),
custom_uri = NULL,
use_local_fallback = TRUE
)
Arguments
- source
Where to get the PSI-MS CV from: - 'latest' will download 'psi-ms.obo' from https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest - 'local' will use rmzqc/cv/psi-ms.obo' (which might be outdated, if you need the latest terms) - 'custom' uses a user-defined URI in 'custom_uri'
- custom_uri
Used when 'source' is set to 'custom'. The URI can be local or remote, e.g. 'c:/obo/my.obo' or 'https://www.abc.com/my.obo'
- use_local_fallback
When downloading a file from a URI fails, should we fall back to the local psi-ms.obo shipped with rmzqc?