Skip to contents

Compound Annotation Sources for CompDb databases

Source: R/CompDbSource.R
CompDbSource.Rd

CompDbSource objects represent references to CompoundDb::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 matchSpectra method.

New 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 dbfile.

  • 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") and ... which allows to pass optional parameters to the AnnotationHub constructor function, such as localHub = TRUE to use only the cached data and avoid updating/retrieving updates from the internet.

Other functions:

  • metadata: get metadata (information) on the annotation resource.

Usage

CompDbSource(dbfile = character())

# S4 method for class 'CompDbSource'
metadata(x, ...)

# S4 method for class 'CompDbSource'
show(object)

MassBankSource(release = "2021.03", ...)

Arguments

dbfile

character(1) with the database file (including the full path).

x

A CompDbSource object.

...

For CompDbSource: ignored. For MassBankSource: optional parameters passed to the AnnotationHub constructor function.

object

A CompDbSource object.

release

A character(1) defining the version/release of MassBank that should be used.

Author

Johannes Rainer

Examples


## 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
#> Object of class CompDbSource 
#> Metadata information:
#>   - source: MassBank
#>   - url: https://massbank.eu/MassBank/
#>   - source_version: 2020.09
#>   - source_date: 1603272565
#>   - organism: NA
#>   - db_creation_date: Thu Oct 22 08:45:31 2020
#>   - supporting_package: CompoundDb
#>   - supporting_object: CompDb

## Retrieve a CompDb with MassBank data for a certain MassBank release
mb_src <- MassBankSource("2021.03")
mb_src
#> Object of class CompDbSource 
#> Metadata information:
#>   - source: MassBank
#>   - url: https://massbank.eu/MassBank/
#>   - source_version: 2021.03
#>   - source_date: 2021-02-26
#>   - organism: NA
#>   - db_creation_date: Tue Aug 30 06:53:53 2022
#>   - supporting_package: CompoundDb
#>   - supporting_object: CompDb