S4 generic functions for Bioconductor proteomics infrastructure

Description

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.

Usage

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, ...)

Arguments

Details

list(list("When should one define a generics?"), list(" ", " ", " Generics are appropriate for functions that have ", list("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 ", list("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. ",

"

", " "))

list(list("When to define a generic in ", list("ProtGenerics"), "?"), list(" ", "
", " ", list("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 ", list("mzR::psms"), " and ", " ", list("mzID::psms"), ", or ", list("IRanges::score"), " and ", list("mzR::score"), ", ", " now ", list(

"BioGenerics::score"), ") or generics that live in a rather big

", " package (say ", list("mzR"), ") on which one wouldn't want to depend just ", " for the sake of that generics' definition. ", " ", " ", " The goal of ", list("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 ", list("ProtGenerics"),

", (2)

", " remove the definitions from the packages they stem from, which then ", " (3) only need to import ", list("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: ", "
", " ", list("https://github.com/lgatto/ProtGenerics"), " ", " ", " "))

Seealso

• 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.

• setGeneric and setMethod for defining generics and methods.

Author

Laurent Gatto lg390@cam.ac.uk

Examples

## List all the symbols defined in this package:
ls('package:ProtGenerics')

## What methods exists for 'peaks'
showMethods("peaks")

## To look at one method in particular
getMethod("peaks", "mzRpwiz")