CompDbSource objects represent references to CompDb database-backed
annotation resources. Instances are expected to be created with the dedicated
construction functions such as
MassBankSource or the generic
CompDbSource. The annotation data is not stored within the object but will
be accessed/loaded within the object's
CompDbSource objects can be created using the functions:
CompDbSource: create a new
CompDbSource object from an existing
CompDb database. The (SQLite) database file (including the full path)
needs to be provided with parameter
MassBankSource: retrieves a
CompDb database for the specified MassBank
release from Bioconductor's online
AnnotationHub (if it exists) and
uses that. Note that
AnnotationHub resources are cached locally and thus
only downloaded the first time.
The function has parameters
release which allows to define the desired
MassBank release (e.g.
release = "2021.03" or
release = "2022.06")
... which allows to pass optional parameters to the
constructor function, such as
localHub = TRUE to use only the cached
data and avoid updating/retrieving updates from the internet.
metadata: get metadata (information) on the annotation resource.
CompDbSource(dbfile = character()) ## S4 method for signature 'CompDbSource' metadata(x, ...) ## S4 method for signature 'CompDbSource' show(object) MassBankSource(release = "2021.03", ...)
## Locate a CompDb SQLite database file. For this example we use the test ## database from the `CompoundDb` package. fl <- system.file("sql", "CompDb.MassBank.sql", package = "CompoundDb") ann_src <- CompDbSource(fl) ## The object contains only the reference/link to the annotation resource. ann_src ## Retrieve a CompDb with MassBank data for a certain MassBank release mb_src <- MassBankSource("2021.03") mb_src
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