README.md

In lgatto/ProtGenerics: Generic infrastructure for Bioconductor mass spectrometry packages

Generic infrastructure for Bioconductor mass spectrometry packages

Description:

These generic functions and classes provide basic interfaces to operations on and data access to 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, ...)
## and many more - see below

Arguments:

• object: Object of class for which methods are defined.
• ...: Further arguments, possibly used by downstream methods.

Details:

When should one define a generics?:

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.

When to define a generic in ProtGenerics?:

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 mzR::psms and mzID::psms, or IRanges::score and mzR::score, now BioGenerics::score) or generics that live in a rather big package (say 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 ProtGenerics, (2) 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:

https://github.com/RforMassSpectrometry/ProtGenerics

See Also:

• 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.

Examples:

library("ProtGenerics")
## 
## Attaching package: 'ProtGenerics'
## The following object is masked from 'package:stats':
## 
##     smooth
## List all the symbols defined in this package:
ls('package:ProtGenerics')
##   [1] "accessions"                "acquisitionNum"           
##   [3] "addProcessing"             "adjacencyMatrix"          
##   [5] "aggregateFeatures"         "alignRt"                  
##   [7] "analyser"                  "analyserDetails"          
##   [9] "analyzer"                  "analyzerDetails"          
##  [11] "as.list"                   "bin"                      
##  [13] "calculateFragments"        "centroided"               
##  [15] "centroided<-"              "chromatogram"             
##  [17] "chromatograms"             "collisionEnergy"          
##  [19] "collisionEnergy<-"         "combineFeatures"          
##  [21] "compareChromatograms"      "compareSpectra"           
##  [23] "compounds"                 "database"                 
##  [25] "dataOrigin"                "dataOrigin<-"             
##  [27] "dataStorage"               "dataStorage<-"            
##  [29] "detectorType"              "executeProcessingStep"    
##  [31] "expemail"                  "exptitle"                 
##  [33] "filterAcquisitionNum"      "filterDataOrigin"         
##  [35] "filterDataStorage"         "filterEmptySpectra"       
##  [37] "filterIntensity"           "filterIsolationWindow"    
##  [39] "filterMsLevel"             "filterMz"                 
##  [41] "filterNA"                  "filterPolarity"           
##  [43] "filterPrecursorCharge"     "filterPrecursorMz"        
##  [45] "filterPrecursorScan"       "filterProductMz"          
##  [47] "filterRt"                  "impute"                   
##  [49] "instrumentCustomisations"  "instrumentManufacturer"   
##  [51] "instrumentModel"           "intensity"                
##  [53] "intensity<-"               "ionCount"                 
##  [55] "ions"                      "ionSource"                
##  [57] "ionSourceDetails"          "isCentroided"             
##  [59] "isolationWindowLowerMz"    "isolationWindowLowerMz<-" 
##  [61] "isolationWindowTargetMz"   "isolationWindowTargetMz<-"
##  [63] "isolationWindowUpperMz"    "isolationWindowUpperMz<-" 
##  [65] "mass"                      "modifications"            
##  [67] "msInfo"                    "msLevel"                  
##  [69] "msLevel<-"                 "mz"                       
##  [71] "mz<-"                      "peaks"                    
##  [73] "peaks<-"                   "peptides"                 
##  [75] "polarity"                  "polarity<-"               
##  [77] "precAcquisitionNum"        "precScanNum"              
##  [79] "precursorCharge"           "precursorCharge<-"        
##  [81] "precursorIntensity"        "precursorIntensity<-"     
##  [83] "precursorMz"               "precursorMz<-"            
##  [85] "processingData"            "processingData<-"         
##  [87] "ProcessingStep"            "productMz"                
##  [89] "productMz<-"               "proteins"                 
##  [91] "psms"                      "quantify"                 
##  [93] "rtime"                     "rtime<-"                  
##  [95] "scanIndex"                 "scans"                    
##  [97] "smooth"                    "smoothed"                 
##  [99] "smoothed<-"                "spectra"                  
##  [ reached getOption("max.print") -- omitted 11 entries ]

library("mzR")
## Loading required package: Rcpp
## What methods exists for 'peaks'
showMethods("peaks")
## Function: peaks (package ProtGenerics)
## object="mzRnetCDF"
## object="mzRpwiz"

## To look at one method in particular
getMethod("peaks", "mzRpwiz")
## Method Definition:
## 
## function (object, ...) 
## {
##     .local <- function (object, scans) 
##     .peaks(object, scans)
##     .local(object, ...)
## }
## <bytecode: 0x562747dab008>
## <environment: namespace:mzR>
## 
## Signatures:
##         object   
## target  "mzRpwiz"
## defined "mzRpwiz"

lgatto/ProtGenerics documentation built on March 14, 2024, 7:06 a.m.