BiocGenerics-package: S4 generic functions for Bioconductor

In BiocGenerics: S4 generic functions used in Bioconductor

Description

S4 generic functions needed by many Bioconductor packages.

Details

We divide the generic functions defined in the BiocGenerics package in 2 categories: (1) functions already defined in base R and explicitly promoted to generics in BiocGenerics, and (2) Bioconductor specific generics.

(1) Functions defined in base R and explicitly promoted to generics in the BiocGenerics package

Generics for functions defined in package base:

• BiocGenerics::append

• BiocGenerics::as.data.frame

• BiocGenerics::as.list

• BiocGenerics::as.vector

• BiocGenerics::rbind, BiocGenerics::cbind

• BiocGenerics::colSums, BiocGenerics::rowSums, BiocGenerics::colMeans, BiocGenerics::rowMeans

• BiocGenerics::do.call

• BiocGenerics::duplicated, BiocGenerics::anyDuplicated

• BiocGenerics::eval

• Extremes: BiocGenerics::pmax, BiocGenerics::pmin, BiocGenerics::pmax.int, BiocGenerics::pmin.int

• funprog: BiocGenerics::Reduce, BiocGenerics::Filter, BiocGenerics::Find, BiocGenerics::Map, BiocGenerics::Position

• BiocGenerics::get, BiocGenerics::mget

• BiocGenerics::grep, BiocGenerics::grepl

• BiocGenerics::is.unsorted

• BiocGenerics::lapply, BiocGenerics::sapply

• BiocGenerics::mapply

• BiocGenerics::match, BiocGenerics::%in%

• BiocGenerics::nrow, BiocGenerics::ncol, BiocGenerics::NROW, BiocGenerics::NCOL

• BiocGenerics::order

• BiocGenerics::paste

• BiocGenerics::rank

• BiocGenerics::rep.int

• BiocGenerics::rownames, BiocGenerics::rownames<-, BiocGenerics::colnames, BiocGenerics::colnames<-

• sets: BiocGenerics::union, BiocGenerics::intersect, BiocGenerics::setdiff

• BiocGenerics::sort

• BiocGenerics::start, BiocGenerics::start<-, BiocGenerics::end, BiocGenerics::end<-, BiocGenerics::width, BiocGenerics::width<-, BiocGenerics::pos

• BiocGenerics::subset

• BiocGenerics::table

• BiocGenerics::tapply

• BiocGenerics::unique

• BiocGenerics::unlist

• BiocGenerics::unsplit

• BiocGenerics::which

• BiocGenerics::which.min, BiocGenerics::which.max

Generics for functions defined in package utils:

• BiocGenerics::relist

Generics for functions defined in package graphics:

• BiocGenerics::boxplot

• BiocGenerics::image

Generics for functions defined in package stats:

• BiocGenerics::density

• BiocGenerics::residuals

• BiocGenerics::weights

• BiocGenerics::xtabs

Generics for functions defined in package parallel:

• BiocGenerics::clusterCall, BiocGenerics::clusterApply, BiocGenerics::clusterApplyLB, BiocGenerics::clusterEvalQ, BiocGenerics::clusterExport, BiocGenerics::clusterMap, BiocGenerics::clusterSplit, BiocGenerics::parLapply, BiocGenerics::parSapply, BiocGenerics::parApply, BiocGenerics::parRapply, BiocGenerics::parCapply, BiocGenerics::parLapplyLB, BiocGenerics::parSapplyLB

(2) Bioconductor specific generics

• annotation, annotation<-

• combine

• dbconn, dbfile

• dims

• fileName

• normalize

• Ontology

• organism, organism<-, species, species<-

• path, path<-, basename, basename<-, dirname, dirname<-

• plotMA

• plotPCA

• score, score<-

• strand, strand<-, invertStrand

• toTable

• type, type<-

• updateObject

Note

More generics can be added on request by sending an email to the Bioc-devel mailing list:

http://bioconductor.org/help/mailing-list/

Things that should NOT be added to the BiocGenerics package:

• Internal generic primitive functions like length, dim, `dim<-`, etc... See ?InternalMethods for the complete list. There are a few exceptions though, that is, the BiocGenerics package may actually redefine a few of those internal generic primitive functions as S4 generics when for example the signature of the internal generic primitive is not appropriate (this is the case for BiocGenerics::cbind).

• S3 and S4 group generic functions like Math, Ops, etc... See ?groupGeneric and ?S4groupGeneric for the complete list.

• Generics already defined in the stats4 package.

Author(s)

The Bioconductor Dev Team

See Also

• 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

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

Example output

Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

  [1] "Filter"                "Find"                  "IQR"                  
  [4] "Map"                   "NCOL"                  "NROW"                 
  [7] "Position"              "Reduce"                "annotation"           
 [10] "annotation<-"          "anyDuplicated"         "append"               
 [13] "as.data.frame"         "as.list"               "as.vector"            
 [16] "boxplot"               "cbind"                 "clusterApply"         
 [19] "clusterApplyLB"        "clusterCall"           "clusterEvalQ"         
 [22] "clusterExport"         "clusterMap"            "clusterSplit"         
 [25] "colMeans"              "colSums"               "colnames"             
 [28] "colnames<-"            "combine"               "conditions"           
 [31] "conditions<-"          "counts"                "counts<-"             
 [34] "dbconn"                "dbfile"                "density"              
 [37] "design"                "design<-"              "dispTable"            
 [40] "dispTable<-"           "do.call"               "duplicated"           
 [43] "end"                   "end<-"                 "estimateDispersions"  
 [46] "estimateSizeFactors"   "eval"                  "evalq"                
 [49] "fileName"              "get"                   "getObjectSlots"       
 [52] "grep"                  "grepl"                 "image"                
 [55] "intersect"             "invertStrand"          "is.unsorted"          
 [58] "lapply"                "lengths"               "mad"                  
 [61] "mapply"                "match"                 "mean"                 
 [64] "mget"                  "ncol"                  "normalize"            
 [67] "nrow"                  "order"                 "organism"             
 [70] "organism<-"            "parApply"              "parCapply"            
 [73] "parLapply"             "parLapplyLB"           "parRapply"            
 [76] "parSapply"             "parSapplyLB"           "paste"                
 [79] "plotDispEsts"          "plotMA"                "plotPCA"              
 [82] "pmax"                  "pmax.int"              "pmin"                 
 [85] "pmin.int"              "rank"                  "rbind"                
 [88] "relist"                "rep.int"               "residuals"            
 [91] "rowMeans"              "rowSums"               "rownames"             
 [94] "rownames<-"            "sapply"                "score"                
 [97] "score<-"               "sd"                    "setdiff"              
[100] "sizeFactors"           "sizeFactors<-"         "sort"                 
[103] "species"               "species<-"             "start"                
[106] "start<-"               "strand"                "strand<-"             
[109] "subset"                "t"                     "table"                
[112] "tapply"                "union"                 "unique"               
[115] "unlist"                "unsplit"               "unstrand"             
[118] "updateObject"          "updateObjectFromSlots" "var"                  
[121] "weights"               "which"                 "which.max"            
[124] "which.min"             "width"                 "width<-"              
[127] "xtabs"                

BiocGenerics documentation built on April 17, 2021, 6:01 p.m.