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Compound Annotation Sources

Source: R/CompAnnotationSource.R
CompAnnotationSource.Rd

CompAnnotationSources (i.e. classes extending the base virtual CompAnnotationSource class) define and provide access to a (potentially remote) compound annotation resource. This aims to simplify the integration of external annotation resources by automating the actual connection (or data resource download) process from the user. In addition, since the reference resource is not directly exposed to the user it allows integration of annotation resources that do not allow access to the full data.

Objects extending CompAnnotationSource available in this package are:

  • CompDbSource(): annotation source referencing an annotation source in the [CompoundDb::CompDb()] format ( from the CompoundDb Bioconductor package).

Classes extending CompAnnotationSource need to implement the matchSpectra method with parameters query, target and param where query is the Spectra object with the (experimental) query spectra, target the object extending the CompAnnotationSource and param the parameter object defining the similarity calculation (e.g. CompareSpectraParam(). The method is expected to return a MatchedSpectra object.

CompAnnotationSource objects are not expected to contain any annotation data. Access to the annotation data (in form of a Spectra object) is suggested to be only established within the object's matchSpectra method. This would also enable parallel processing of annotations as no e.g. database connection would have to be shared across processes.

Usage

# S4 method for class 'Spectra,CompAnnotationSource,Param'
matchSpectra(query, target, param, ...)

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

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

Arguments

query

for matchSpectra: Spectra::Spectra object with the query spectra.

target

for matchSpectra: object extending CompAnnotationSource (such as CompDbSource) with the target (reference) spectra to compare query against.

param

for matchSpectra: parameter object (such as CompareSpectraParam) defining the settings for the matching.

...

additional parameters passed to matchSpectra.

object

A CompAnnotationSource object.

x

A CompAnnotationSource object.

Methods that need to be implemented

For an example implementation see CompDbSource().

  • matchSpectra: function to match experimental MS2 spectra against the annotation source. See matchSpectra() for parameters.

  • metadata: function to provide metadata on the annotation resource (host, source, version etc).

  • show (optional): method to provide general information on the data source.

Author

Johannes Rainer, Nir Shachaf