These generic functions provide basic interfaces to operations on and data access to proteomics and mass spectrometry infrastructure in the Bioconductor project.
For the details, please consult the respective methods' manual pages.
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psms(object, ...) peaks(object, ...) modifications(object, ...) database(object, ...) rtime(object, ...) tic(object, ...) spectra(object, ...) intensity(object, ...) mz(object, ...) peptides(object, ...) proteins(object, ...) accessions(object, ...) scans(object, ...) mass(object, ...) ions(object, ...) chromatograms(object, ...) chromatogram(object, ...) isCentroided(object, ...) writeMSData(object, file, ...)
Object of class for which methods are defined.
: the name of the file to which the data should be exported.
Further arguments, possibly used by downstream methods.
Generics are appropriate for functions that have generic
names, i.e. names that occur in multiple circumstances, (with
different input classes, most often defined in different packages)
or, when (multiple) dispatching is better handled by the generics
mechanism rather than the developer. The dispatching mechanism will
then automatically call the appropriate method and save the user
from explicitly calling
package::method or the developer to
handle the multiple input types cases. When no such conflict exists
or is unlikely to happen (for example when the name of the function
is specific to a package or domain, or for class slots accessors and
replacement methods), the usage of a generic is arguably
questionable, and in most of these cases, simple, straightforward
functions would be perfectly valid.
ProtGenerics is not meant to be the central package for
generics, nor should it stop developers from defining the generics
they need. It is a means to centralise generics that are defined in
different packages (for example
BioGenerics::score) or generics that live in a rather big
mzR) on which one wouldn't want to depend just
for the sake of that generics' definition.
The goal of
ProtGenerics is to step in when namespace
conflicts arise so as to to facilitate inter-operability of
packages. In case such conflict appears due to multiple generics, we
would (1) add these same definitions in
remove the definitions from the packages they stem from, which then
(3) only need to import
ProtGenerics. This would be very
minor/straightforward changes for the developers and would resolve
issues when they arise.
More generics can be added on request by opening an issue or sending a pull request on:
The BiocGenerics package for S4 generic functions needed by many Bioconductor packages.
showMethods for displaying a summary of
the methods defined for a given generic function.
selectMethod for getting the definition of
a specific method.
setMethod for defining generics and methods.
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