Package 'BiocGenerics'

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 or in CRAN package generics, and explicitly promoted to S4 generics in BiocGenerics

2. S4 generics specific to Bioconductor.

(1) Functions defined in base R or CRAN package generics and explicitly promoted to S4 generics in the BiocGenerics package

Generics for functions defined in package base:

• BiocGenerics::aperm

• BiocGenerics::append

• BiocGenerics::as.data.frame

• BiocGenerics::as.list

• BiocGenerics::as.vector

• BiocGenerics::rbind, BiocGenerics::cbind

• BiocGenerics::do.call

• BiocGenerics::duplicated, BiocGenerics::anyDuplicated

• BiocGenerics::eval

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

• BiocGenerics::format

• 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<-

• BiocGenerics::saveRDS

• BiocGenerics::sort

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

• BiocGenerics::subset

• BiocGenerics::t

• 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 CRAN package generics:

• setops: BiocGenerics::union, BiocGenerics::intersect, BiocGenerics::setdiff, BiocGenerics::setequal

(2) S4 generics specific to Bioconductor

• annotation, annotation<-

• combine

• containsOutOfMemoryData

• dbconn, dbfile

• counts, counts<-, design, design<-, dispTable, dispTable<-, sizeFactors, sizeFactors<-, conditions, conditions<-, estimateSizeFactors, estimateDispersions, plotDispEsts

• dims, nrows, ncols,

• fileName

• normalize

• Ontology

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

• paste2

• 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')

Description

Get or set the annotation information contained in an object.

Usage

annotation(object, ...)
annotation(object, ...) <- value

Arguments

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.

• annotation,eSet-method in the Biobase package for an example of a specific annotation method (defined for eSet objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

annotation
showMethods("annotation")

library(Biobase)
showMethods("annotation")
selectMethod("annotation", "eSet")

Description

Transpose an array-like object by permuting its dimensions.

This is a multidimensional generalization of the t() operator used for 2D-transposition.

NOTE: This man page is for the aperm S4 generic function defined in the BiocGenerics package. See ?base::aperm for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

aperm(a, perm, ...)

Arguments

Value

A transposed version of array-like object a, with subscripts permuted as indicated by the perm vector.

See Also

• base::aperm for the default aperm method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• aperm,SVT_SparseArray-method in the SparseArray package for an example of a specific aperm method (defined for SVT_SparseArray objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

aperm  # note the dispatch on the 'a' arg only
showMethods("aperm")
selectMethod("aperm", "ANY")  # the default method

Description

Append (or insert) elements to (in) a vector-like object.

NOTE: This man page is for the append S4 generic function defined in the BiocGenerics package. See ?base::append for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like or data-frame-like) not supported by the default method.

Usage

append(x, values, after=length(x))

Arguments

Value

See ?base::append for the value returned by the default method.

Specific methods defined in Bioconductor packages will typically return an object of the same class as x and of length length(x) + length(values).

See Also

• base::append for the default append method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• append,Vector,Vector-method in the S4Vectors package for an example of a specific append method (defined for Vector objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

append  # note the dispatch on the 'x' and 'values' args only
showMethods("append")
selectMethod("append", c("ANY", "ANY"))  # the default method

Description

Generic function to coerce to a data frame, if possible.

NOTE: This man page is for the as.data.frame S4 generic function defined in the BiocGenerics package. See ?base::as.data.frame for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

as.data.frame(x, row.names=NULL, optional=FALSE, ...)

Arguments

Value

An ordinary data frame.

See ?base::as.data.frame for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::as.data.frame for the default as.data.frame method.

• toTable for an alternative to as.data.frame.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• as.data.frame,DataFrame-method in the S4Vectors package, and as.data.frame,IntegerRanges-method in the IRanges package, for examples of specific as.data.frame methods (defined for DataFrame and IntegerRanges objects, respectively).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

as.data.frame  # note the dispatch on the 'x' arg only
showMethods("as.data.frame")
selectMethod("as.data.frame", "ANY")  # the default method

Description

Generic function to coerce to a list, if possible.

NOTE: This man page is for the as.list S4 generic function defined in the BiocGenerics package. See ?base::as.list for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

as.list(x, ...)

Arguments

Value

An ordinary list.

See Also

• base::as.list for the default as.list method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• as.list,List-method in the S4Vectors package for an example of a specific as.list method (defined for List objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

as.list
showMethods("as.list")
selectMethod("as.list", "ANY")  # the default method

library(S4Vectors)
showMethods("as.list")
## The as.list() method for List objects:
selectMethod("as.list", "List")

Description

Attempt to coerce an object into a vector of the specified mode. If the mode is not specified, attempt to coerce to whichever vector mode is considered more appropriate for the class of the supplied object.

NOTE: This man page is for the as.vector S4 generic function defined in the BiocGenerics package. See ?base::as.vector for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

as.vector(x, mode="any")

Arguments

Value

A vector.

See ?base::as.vector for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::as.vector for the default as.vector method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• as.vector,Rle-method in the S4Vectors package, and as.vector,AtomicList-method in the IRanges packages, for examples of specific as.vector methods (defined for Rle and AtomicList objects, respectively).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

as.vector  # note the dispatch on the 'x' arg only
showMethods("as.vector")
selectMethod("as.vector", "ANY")  # the default method

Description

Produce box-and-whisker plot(s) of the given (grouped) values.

NOTE: This man page is for the boxplot S4 generic function defined in the BiocGenerics package. See ?graphics::boxplot for the default method (defined in the graphics package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

boxplot(x, ...)

Arguments

Value

See ?graphics::boxplot for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• graphics::boxplot for the default boxplot method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• boxplot,AffyBatch-method in the affy package for an example of a specific boxplot method (defined for AffyBatch objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

boxplot
showMethods("boxplot")
selectMethod("boxplot", "ANY")  # the default method

library(affy)
showMethods("boxplot")
## The boxplot() method for AffyBatch objects:
selectMethod("boxplot", "AffyBatch")

Description

rbind and cbind take one or more objects and combine them by columns or rows, respectively.

NOTE: This man page is for the rbind and cbind S4 generic functions defined in the BiocGenerics package. See ?base::cbind for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like or matrix-like) not supported by the default methods.

Usage

rbind(..., deparse.level=1)
cbind(..., deparse.level=1)

Arguments

Value

See ?base::cbind for the value returned by the default methods.

Specific methods defined in Bioconductor packages will typically return an object of the same class as the input objects.

See Also

• base::cbind for the default rbind and cbind methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• rbind,RectangularData-method and cbind,DataFrame-method in the S4Vectors package for examples of specific rbind and cbind methods (defined for RectangularData derivatives and DataFrame objects, respectively).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

rbind  # note the dispatch on the '...' arg only
showMethods("rbind")
selectMethod("rbind", "ANY")  # the default method

cbind  # note the dispatch on the '...' arg only
showMethods("cbind")
selectMethod("cbind", "ANY")  # the default method

library(S4Vectors)
showMethods("rbind")
## The rbind() method for RectangularData derivatives:
selectMethod("rbind", "RectangularData")
## The cbind() method for DataFrame objects:
selectMethod("cbind", "DataFrame")

Description

The combine generic function handles methods for combining or merging different Bioconductor data structures. It should, given an arbitrary number of arguments of the same class (possibly by inheritance), combine them into a single instance in a sensible way (some methods may only combine 2 objects, ignoring ... in the argument list; because Bioconductor data structures are complicated, check carefully that combine does as you intend).

Usage

combine(x, y, ...)

Arguments

Details

There are two basic combine strategies. One is an intersection strategy. The returned value should only have rows (or columns) that are found in all input data objects. The union strategy says that the return value will have all rows (or columns) found in any one of the input data objects (in which case some indication of what to use for missing values will need to be provided).

These functions and methods are currently under construction. Please let us know if there are features that you require.

Value

A single value of the same class as the most specific common ancestor (in class terms) of the input values. This will contain the appropriate combination of the data in the input values.

Methods

The following methods are defined in the BiocGenerics package:

combine(x=ANY, missing)

Return the first (x) argument unchanged.

combine(data.frame, data.frame)

Combines two data.frame objects so that the resulting data.frame contains all rows and columns of the original objects. Rows and columns in the returned value are unique, that is, a row or column represented in both arguments is represented only once in the result. To perform this operation, combine makes sure that data in shared rows and columns are identical in the two data.frames. Data differences in shared rows and columns usually cause an error. combine issues a warning when a column is a factor and the levels of the factor in the two data.frames are different.

combine(matrix, matrix)

Combined two matrix objects so that the resulting matrix contains all rows and columns of the original objects. Both matricies must have dimnames. Rows and columns in the returned value are unique, that is, a row or column represented in both arguments is represented only once in the result. To perform this operation, combine makes sure that data in shared rows and columns are all equal in the two matricies.

Additional combine methods are defined in the Biobase package for AnnotatedDataFrame, AssayData, MIAME, and eSet objects.

Author(s)

Biocore

See Also

• combine,AnnotatedDataFrame,AnnotatedDataFrame-method, combine,AssayData,AssayData-method, combine,MIAME,MIAME-method, and combine,eSet,eSet-method in the Biobase package for additional combine methods.

• merge for merging two data frames (or data-frame-like) objects.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

combine
showMethods("combine")
selectMethod("combine", c("ANY", "missing"))
selectMethod("combine", c("data.frame", "data.frame"))
selectMethod("combine", c("matrix", "matrix"))

## ---------------------------------------------------------------------
## COMBINING TWO DATA FRAMES
## ---------------------------------------------------------------------
x <- data.frame(x=1:5,
        y=factor(letters[1:5], levels=letters[1:8]),
        row.names=letters[1:5])
y <- data.frame(z=3:7,
        y=factor(letters[3:7], levels=letters[1:8]),
        row.names=letters[3:7])
combine(x,y)

w <- data.frame(w=4:8,
       y=factor(letters[4:8], levels=letters[1:8]),
       row.names=letters[4:8])
combine(w, x, y)

# y is converted to 'factor' with different levels
df1 <- data.frame(x=1:5,y=letters[1:5], row.names=letters[1:5])
df2 <- data.frame(z=3:7,y=letters[3:7], row.names=letters[3:7])
try(combine(df1, df2)) # fails
# solution 1: ensure identical levels
y1 <- factor(letters[1:5], levels=letters[1:7])
y2 <- factor(letters[3:7], levels=letters[1:7])
df1 <- data.frame(x=1:5,y=y1, row.names=letters[1:5])
df2 <- data.frame(z=3:7,y=y2, row.names=letters[3:7])
combine(df1, df2)
# solution 2: force column to be 'character'
df1 <- data.frame(x=1:5,y=I(letters[1:5]), row.names=letters[1:5])
df2 <- data.frame(z=3:7,y=I(letters[3:7]), row.names=letters[3:7])
combine(df1, df2)

## ---------------------------------------------------------------------
## COMBINING TWO MATRICES
## ---------------------------------------------------------------------
m <- matrix(1:20, nrow=5, dimnames=list(LETTERS[1:5], letters[1:4]))
combine(m[1:3,], m[4:5,])
combine(m[1:3, 1:3], m[3:5, 3:4]) # overlap

Description

Some objects in Bioconductor can use on-disk or other out-of-memory representation for their data, typically (but not necessarily) when the data is too big to fit in memory. For example the data in a TxDb object is stored in an SQLite database, and the data in an HDF5Array object is stored in an HDF5 file.

The containsOutOfMemoryData() function determines whether an object contains out-of-memory data or not.

Note that objects with out-of-memory data are usually not compatible with a serialization/unserialization roundtrip. More concretely, base::saveRDS()/base::readRDS() tend to silently break them!

See ?saveHDF5SummarizedExperiment in the HDF5Array package for a more extensive discussion about this.

Usage

containsOutOfMemoryData(object)

Arguments

Details

An object can store some of its data on disk and some of it in memory. This is the case for example when a SummarizedExperiment object (or derivative) has some of its assays on disk (e.g. in HDF5Matrix objects) and others in memory (e.g. in ordinary matrices and/or SparseMatrix objects).

Of course in this case, containsOutOfMemoryData() will still return TRUE. In other words, containsOutOfMemoryData(object) will only return FALSE when all the data in object resides in memory, that is, when the object can safely be serialized.

Value

TRUE or FALSE.

Note

TO DEVELOPERS:

The BiocGenerics package also defines the following:

• A default containsOutOfMemoryData() method that returns TRUE if object is an S4 object with at least one slot for which containsOutOfMemoryData() is TRUE (recursive definition), and FALSE otherwise.

• A containsOutOfMemoryData() method for list objects that returns TRUE if object has at least one list element for which containsOutOfMemoryData() is TRUE (recursive definition), and FALSE otherwise.

• A containsOutOfMemoryData() method for environment objects that returns TRUE if object contains at least one object for which containsOutOfMemoryData() is TRUE (recursive definition), and FALSE otherwise.

• The OutOfMemoryObject class. This is a virtual S4 class with no slots that any class defined in Bioconductor that represents out-of-memory objects should extend.

• A containsOutOfMemoryData() method for OutOfMemoryObject derivatives that returns TRUE.

Therefore, if you implement a class that uses an out-of-memory representation, make sure that it contains the OutOfMemoryObject class. This will make containsOutOfMemoryData() return TRUE on your objects, so you don't need to define a containsOutOfMemoryData() method for them.

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.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

containsOutOfMemoryData
showMethods("containsOutOfMemoryData")

## The default method:
selectMethod("containsOutOfMemoryData", "ANY")

## The method for list objects:
selectMethod("containsOutOfMemoryData", "list")

## The method for OutOfMemoryObject derivatives:
selectMethod("containsOutOfMemoryData", "OutOfMemoryObject")

m <- matrix(0, nrow=7, ncol=10)
m[sample(length(m), 20)] <- runif(20)
containsOutOfMemoryData(m)  # FALSE

library(SparseArray)
svt <- as(m, "SparseArray")
svt
containsOutOfMemoryData(m)  # FALSE
containsOutOfMemoryData(list(m, svt))  # FALSE

library(HDF5Array)
M <- as(m, "HDF5Array")
M
containsOutOfMemoryData(M)  # TRUE
containsOutOfMemoryData(list(m, svt, M))  # TRUE

Description

Get a connection object or file path for a SQLite DB

Usage

dbconn(x)
dbfile(x)

Arguments

Value

dbconn returns a connection object to the SQLite DB containing x's data.

dbfile returns a path (character string) to the SQLite DB (file) containing x's data.

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.

• dbconn,AnnotationDb-method in the AnnotationDbi package for an example of a specific dbconn method (defined for dbconn objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

dbconn
showMethods("dbconn")
dbfile
showMethods("dbfile")

library(AnnotationDbi)
showMethods("dbconn")
selectMethod("dbconn", "AnnotationDb")

Description

The generic function density computes kernel density estimates.

NOTE: This man page is for the density S4 generic function defined in the BiocGenerics package. See ?stats::density for the default method (defined in the stats package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

density(x, ...)

Arguments

Value

See ?stats::density for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• stats::density for the default density method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• density,flowClust-method in the flowClust package for an example of a specific density method (defined for flowClust objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

density
showMethods("density")
selectMethod("density", "ANY")  # the default method

Description

These generic functions provide basic interfaces to operations on and data access to count datasets.

Usage

counts(object, ...)
counts(object, ...) <- value
design(object, ...)
design(object, ...) <- value
dispTable(object, ...)
dispTable(object, ...)  <- value
sizeFactors(object, ...)
sizeFactors(object, ...) <- value
conditions(object, ...)
conditions(object, ...) <- value
estimateSizeFactors(object, ...)
estimateDispersions(object, ...)
plotDispEsts(object, ...)

Arguments

Details

For the details, please consult the manual pages of the methods in the DESeq, DESeq2, and DEXSeq packages and the package vignettes.

Author(s)

W. Huber, S. Anders

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.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Description

Get the dimensions, number of rows, or number of columns, of each element of a list-like object.

Note that these functions are the vectorized versions of corresponding functions dim(), nrow(), and ncol(), in the same fashion that lengths() is the vectorized version of length.

Usage

dims(x, use.names=TRUE)
nrows(x, use.names=TRUE)
ncols(x, use.names=TRUE)

Arguments

Value

For dims(): Typically a numeric matrix with one row per list element in x and one column per dimension in these list elements (they're all expected to have the same number of dimensions). The i-th row in the returned matrix is a vector containing the dimensions of the i-th list element in x. More formally:

  dims(x)[i, ] is dim(x[[i]])

for any valid i. By default the names on x, if any, are propagated as the rownames of the returned matrix, unless use.names is set to FALSE.

For nrows() or ncols(): A numeric vector with one element per list element in x. The i-th element in the returned vector is the number of rows (or columns) of the i-th list element in x. More formally:

  nrows(x)[i] is nrow(x[[i]]) and ncols(x)[i] is ncol(x[[i]])

for any valid i. By default the names on x, if any, are propagated on the returned vector, unless use.names is set to FALSE.

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.

• dims,DataFrameList-method in the IRanges package for an example of a specific dims method (defined for DataFrameList objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

dims
showMethods("dims")

library(IRanges)
showMethods("dims")
selectMethod("dims", "DataFrameList")

Description

do.call constructs and executes a function call from a name or a function and a list of arguments to be passed to it.

NOTE: This man page is for the do.call S4 generic function defined in the BiocGenerics package. See ?base::do.call for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

do.call(what, args, quote=FALSE, envir=parent.frame())

Arguments

Value

The result of the (evaluated) function call.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::do.call for the default do.call method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

do.call  # note the dispatch on the 'what' and 'args' args only
showMethods("do.call")
selectMethod("do.call", c("ANY", "ANY"))  # the default method

Description

Determines which elements of a vector-like or data-frame-like object are duplicates of elements with smaller subscripts, and returns a logical vector indicating which elements (rows) are duplicates.

NOTE: This man page is for the duplicated and anyDuplicated S4 generic functions defined in the BiocGenerics package. See ?base::duplicated for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like or data-frame-like) not supported by the default method.

Usage

duplicated(x, incomparables=FALSE, ...)
anyDuplicated(x, incomparables=FALSE, ...)

Arguments

Value

The default duplicated method (see ?base::duplicated) returns a logical vector of length N where N is:

• length(x) when x is a vector;

• nrow(x) when x is a data frame.

Specific duplicated methods defined in Bioconductor packages must also return a logical vector of the same length as x when x is a vector-like object, and a logical vector with one element for each row when x is a data-frame-like object.

The default anyDuplicated method (see ?base::duplicated) returns a single non-negative integer and so must the specific anyDuplicated methods defined in Bioconductor packages.

anyDuplicated should always behave consistently with duplicated.

See Also

• base::duplicated for the default duplicated and anyDuplicated methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• duplicated,Rle-method in the S4Vectors package for an example of a specific duplicated method (defined for Rle objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

duplicated
showMethods("duplicated")
selectMethod("duplicated", "ANY")  # the default method

anyDuplicated
showMethods("anyDuplicated")
selectMethod("anyDuplicated", "ANY")  # the default method

Description

eval evaluates an R expression in a specified environment.

NOTE: This man page is for the eval S4 generic function defined in the BiocGenerics package. See ?base::eval for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

eval(expr, envir=parent.frame(),
           enclos=if (is.list(envir) || is.pairlist(envir))
                  parent.frame() else baseenv())

Arguments

Value

See ?base::eval for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::eval for the default eval method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• eval,expression,Vector-method in the IRanges package for an example of a specific eval method (defined for when the expr and envir arguments are an expression and a Vector object, respectively).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

eval  # note the dispatch on 'expr' and 'envir' args only
showMethods("eval")
selectMethod("eval", c("ANY", "ANY"))  # the default method

Description

evalq evaluates an R expression (the quoted form of its first argument) in a specified environment.

NOTE: This man page is for the evalq wrapper defined in the BiocGenerics package. See ?base::evalq for the function defined in the base package. This wrapper correctly delegates to the eval generic, rather than base::eval.

Usage

evalq(expr, envir=parent.frame(),
           enclos=if (is.list(envir) || is.pairlist(envir))
                  parent.frame() else baseenv())

Arguments

Value

See ?base::evalq.

See Also

• base::evalq for the base evalq function.

Examples

evalq  # note just a copy of the original evalq

Description

pmax, pmin, pmax.int and pmin.int return the parallel maxima and minima of the input values.

NOTE: This man page is for the pmax, pmin, pmax.int and pmin.int S4 generic functions defined in the BiocGenerics package. See ?base::pmax for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like or matrix-like) not supported by the default methods.

Usage

pmax(..., na.rm=FALSE)
pmin(..., na.rm=FALSE)
     
pmax.int(..., na.rm=FALSE)
pmin.int(..., na.rm=FALSE)

Arguments

Value

See ?base::pmax for the value returned by the default methods.

Specific methods defined in Bioconductor packages will typically return an object of the same class as the input objects.

See Also

• base::pmax for the default pmax, pmin, pmax.int and pmin.int methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• pmax,Rle-method in the S4Vectors package for an example of a specific pmax method (defined for Rle objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

pmax
showMethods("pmax")
selectMethod("pmax", "ANY")  # the default method

pmin
showMethods("pmin")
selectMethod("pmin", "ANY")  # the default method

pmax.int
showMethods("pmax.int")
selectMethod("pmax.int", "ANY")  # the default method

pmin.int
showMethods("pmin.int")
selectMethod("pmin.int", "ANY")  # the default method

Description

Get the file name of an object.

Usage

fileName(object, ...)

Arguments

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.

• fileName,MSmap-method in the MSnbase package for an example of a specific fileName method (defined for MSmap objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

fileName
showMethods("fileName")

library(MSnbase)
showMethods("fileName")
selectMethod("fileName", "MSmap")

Description

Turn an R object into a character vector used for pretty printing.

NOTE: This man page is for the format S4 generic function defined in the BiocGenerics package. See ?base::format for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

format(x, ...)

Arguments

Value

A character vector that provides a "compact representation" of x. This character vector is typically used by print.data.frame to display the columns of a data.frame object. See ?base::print.data.frame for more information.

See Also

• base::format for the default format method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

format
showMethods("format")
selectMethod("format", "ANY")  # the default method

Description

Reduce uses a binary function to successively combine the elements of a given list-like or vector-like object and a possibly given initial value. Filter extracts the elements of a list-like or vector-like object for which a predicate (logical) function gives true. Find and Position give the first or last such element and its position in the object, respectively. Map applies a function to the corresponding elements of given list-like or vector-like objects.

NOTE: This man page is for the Reduce, Filter, Find, Map and Position S4 generic functions defined in the BiocGenerics package. See ?base::Reduce for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (typically list-like or vector-like) not supported by the default methods.

Usage

Reduce(f, x, init, right=FALSE, accumulate=FALSE, simplify=TRUE)
Filter(f, x)
Find(f, x, right=FALSE, nomatch=NULL)
Map(f, ...)
Position(f, x, right=FALSE, nomatch=NA_integer_)

Arguments

Value

See ?base::Reduce for the value returned by the default methods.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default methods.

See Also

• base::Reduce for the default Reduce, Filter, Find, Map and Position methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• Reduce,List-method in the S4Vectors package for an example of a specific Reduce method (defined for List objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

Reduce  # note the dispatch on the 'x' arg only
showMethods("Reduce")
selectMethod("Reduce", "ANY")  # the default method

Filter  # note the dispatch on the 'x' arg only
showMethods("Filter")
selectMethod("Filter", "ANY")  # the default method

Find  # note the dispatch on the 'x' arg only
showMethods("Find")
selectMethod("Find", "ANY")  # the default method

Map  # note the dispatch on the '...' arg only
showMethods("Map")
selectMethod("Map", "ANY")  # the default method

Position  # note the dispatch on the 'x' arg only
showMethods("Position")
selectMethod("Position", "ANY")  # the default method

Description

Search for an object with a given name and return it.

NOTE: This man page is for the get and mget S4 generic functions defined in the BiocGenerics package. See ?base::get for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (list-like or environment-like) not supported by the default methods.

Usage

get(x, pos=-1, envir=as.environment(pos), mode="any", inherits=TRUE)
mget(x, envir, mode="any", ifnotfound, inherits=FALSE)

Arguments

Details

See ?base::get for details about the default methods.

Value

For get: The value corresponding to the specified key.

For mget: The list of values corresponding to the specified keys. The returned list must have one element per key, and in the same order as in x.

See ?base::get for the value returned by the default methods.

See Also

• base::get for the default get and mget methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• get,ANY,Bimap,missing-method in the AnnotationDbi package for an example of a specific get method (defined for Bimap objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

get  # note the dispatch on the 'x', 'pos' and 'envir' args only
showMethods("get")
selectMethod("get", c("ANY", "ANY", "ANY"))  # the default method

mget  # note the dispatch on the 'x' and 'envir' args only
showMethods("mget")
selectMethod("mget", c("ANY", "ANY"))  # the default method

Description

Search for matches to argument 'pattern' within each element of a character vector.

NOTE: This man page is for the grep and grepl S4 generic functions defined in the BiocGenerics package. See ?base::grep for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE,
          fixed = FALSE, useBytes = FALSE, invert = FALSE)
grepl(pattern, x, ignore.case = FALSE, perl = FALSE,
          fixed = FALSE, useBytes = FALSE)

Arguments

Value

See ?base::grep for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::grep for the default grep and grepl methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

grep  # note the dispatch on 'pattern' and 'x' args only
showMethods("grep")
selectMethod("grep", "ANY")  # the default method

Description

Creates a grid of colored or gray-scale rectangles with colors corresponding to the values in z. This can be used to display three-dimensional or spatial data aka images.

NOTE: This man page is for the image S4 generic function defined in the BiocGenerics package. See ?graphics::image for the default method (defined in the graphics package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

image(x, ...)

Arguments

Details

See ?graphics::image for the details.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• graphics::image for the default image method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• image,AffyBatch-method in the affy package for an example of a specific image method (defined for AffyBatch objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

image
showMethods("image")
selectMethod("image", "ANY")  # the default method

library(affy)
showMethods("image")
## The image() method for AffyBatch objects:
selectMethod("image", "AffyBatch")

Description

Compute the interquartile range for a vector.

NOTE: This man page is for the IQR S4 generic function defined in the BiocGenerics package. See ?stats::IQR for the default method (defined in the stats package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

IQR(x, na.rm = FALSE, type = 7)

Arguments

Value

See ?stats::IQR for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• stats::IQR for the default IQR method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

IQR
showMethods("IQR")
selectMethod("IQR", "ANY")  # the default method

Description

Test if a vector-like object is not sorted, without the cost of sorting it.

NOTE: This man page is for the is.unsorted S4 generic function defined in the BiocGenerics package. See ?base::is.unsorted for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like) not supported by the default method.

Usage

is.unsorted(x, na.rm=FALSE, strictly=FALSE, ...)

Arguments

Value

See ?base::is.unsorted for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

Note

TO DEVELOPERS:

The is.unsorted method for specific vector-like objects should adhere to the same underlying order used by the order, sort, and rank methods for the same objects.

See Also

• base::is.unsorted for the default is.unsorted method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• is.unsorted,GenomicRanges-method in the GenomicRanges package for an example of a specific is.unsorted method (defined for GenomicRanges objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

is.unsorted  # note the dispatch on the 'x' arg only
showMethods("is.unsorted")
selectMethod("is.unsorted", "ANY")  # the default method

Description

lapply returns a list of the same length as X, each element of which is the result of applying FUN to the corresponding element of X.

sapply is a user-friendly version and wrapper of lapply by default returning a vector, matrix or, if simplify="array", an array if appropriate, by applying simplify2array(). sapply(x, f, simplify=FALSE, USE.NAMES=FALSE) is the same as lapply(x, f).

NOTE: This man page is for the lapply and sapply S4 generic functions defined in the BiocGenerics package. See ?base::lapply for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (typically list-like or vector-like) not supported by the default methods.

Usage

lapply(X, FUN, ...)
sapply(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)

Arguments

Value

See ?base::lapply for the value returned by the default methods.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default methods. In particular, lapply and sapply(simplify=FALSE) should always return a list.

See Also

• base::lapply for the default lapply and sapply methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• lapply,List-method in the S4Vectors package for an example of a specific lapply method (defined for List objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

lapply  # note the dispatch on the 'X' arg only
showMethods("lapply")
selectMethod("lapply", "ANY")  # the default method

sapply  # note the dispatch on the 'X' arg only
showMethods("sapply")
selectMethod("sapply", "ANY")  # the default method

Description

Compute the median absolute deviation for a vector, dispatching only on the first argument, x.

NOTE: This man page is for the mad S4 generic function defined in the BiocGenerics package. See ?stats::mad for the default method (defined in the stats package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

mad(x, center = median(x), constant = 1.4826,
    na.rm = FALSE, low = FALSE, high = FALSE)

Arguments

Value

See ?stats::mad for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• stats::mad for the default mad method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

mad
showMethods("mad")
selectMethod("mad", "ANY")  # the default method

Description

mapply is a multivariate version of sapply. mapply applies FUN to the first elements of each ... argument, the second elements, the third elements, and so on. Arguments are recycled if necessary.

NOTE: This man page is for the mapply S4 generic function defined in the BiocGenerics package. See ?base::mapply for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically list-like or vector-like) not supported by the default methods.

Usage

mapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRUE)

Arguments

Value

See ?base::mapply for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::mapply for the default mapply method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

mapply  # note the dispatch on the '...' arg only
showMethods("mapply")
selectMethod("mapply", "ANY")  # the default method

Description

match returns a vector of the positions of (first) matches of its first argument in its second.

%in% is a binary operator that returns a logical vector of the length of its left operand indicating if the elements in it have a match or not.

NOTE: This man page is for the match and %in% S4 generic functions defined in the BiocGenerics package. See ?base::match for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like) not supported by the default methods.

Usage

match(x, table, nomatch=NA_integer_, incomparables=NULL, ...)

x %in% table

Arguments

Value

The same as the default methods (see ?base::match for the value returned by the default methods).

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default methods.

Note

The default base::match method (defined in the base package) doesn't have the ... argument. We've added it to the generic function defined in the BiocGenerics package in order to allow specific methods to support additional arguments if needed.

See Also

• base::match for the default match and %in% methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• match,Hits,Hits-method and %in%,Rle,ANY-method in the S4Vectors package for examples of specific match and %in% methods (defined for Hits and Rle objects, respectively).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

match  # note the dispatch on the 'x' and 'table' args only
showMethods("match")
selectMethod("match", c("ANY", "ANY"))  # the default method

`%in%`
showMethods("%in%")
selectMethod("%in%", c("ANY", "ANY"))  # the default method

Description

Generic function for the (trimmed) arithmetic mean.

NOTE: This man page is for the mean S4 generic function defined in the BiocGenerics package. See ?base::mean for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like) not supported by the default method.

Usage

mean(x, ...)

Arguments

Value

See ?base::mean for the value returned by the default method.

Specific methods defined in Bioconductor packages will typically return an object of the same class as the input object.

See Also

• base::mean for the default mean method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• mean,Rle-method in the S4Vectors package for an example of a specific mean method (defined for Rle objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

mean
showMethods("mean")
selectMethod("mean", "ANY")  # the default method

Description

A generic function which normalizes an object containing microarray data or other data. Normalization is intended to remove from the intensity measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays.

Usage

normalize(object, ...)

Arguments

Value

An object containing the normalized data.

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.

• normalize,AffyBatch-method in the affy package and normalize,MSnExp-method in the MSnbase package for examples of specific normalize methods (defined for AffyBatch and MSnExp objects, respectively).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

normalize
showMethods("normalize")

library(affy)
showMethods("normalize")
selectMethod("normalize", "AffyBatch")

Description

Return the number of rows or columns present in an array-like object.

NOTE: This man page is for the nrow, ncol, NROW and NCOL S4 generic functions defined in the BiocGenerics package. See ?base::nrow for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (typically matrix- or array-like) not supported by the default methods.

Usage

nrow(x)
ncol(x)
NROW(x)
NCOL(x)

Arguments

Value

A single integer or NULL.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default methods.

See Also

• base::nrow for the default nrow, ncol, NROW and NCOL methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• nrow,DataFrame-method in the S4Vectors package for an example of a specific nrow method (defined for DataFrame objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

nrow
showMethods("nrow")
selectMethod("nrow", "ANY")  # the default method

ncol
showMethods("ncol")
selectMethod("ncol", "ANY")  # the default method

NROW
showMethods("NROW")
selectMethod("NROW", "ANY")  # the default method

NCOL
showMethods("NCOL")
selectMethod("NCOL", "ANY")  # the default method

Description

Get the Ontology of an object.

Usage

Ontology(object)

Arguments

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.

• Ontology,GOTerms-method in the AnnotationDbi package for an example of a specific Ontology method (defined for GOTerms objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

Ontology
showMethods("Ontology")

library(AnnotationDbi)
showMethods("Ontology")
selectMethod("Ontology", "GOTerms")

Description

order returns a permutation which rearranges its first argument into ascending or descending order, breaking ties by further arguments.

NOTE: This man page is for the order S4 generic function defined in the BiocGenerics package. See ?base::order for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like) not supported by the default method.

Usage

order(..., na.last=TRUE, decreasing=FALSE, method=c("auto", "shell", "radix"))

Arguments

Value

The default method (see ?base::order) returns an integer vector of length N where N is the common length of the input objects. This integer vector represents a permutation of N elements and can be used to rearrange the first argument in ... into ascending or descending order (by subsetting it).

Specific methods defined in Bioconductor packages should also return an integer vector representing a permutation of N elements.

Note

TO DEVELOPERS:

Specific order methods should preferably be made "stable" for consistent behavior across platforms and consistency with base::order(). Note that C qsort() is not "stable" so order methods that use qsort() at the C-level need to ultimately break ties by position, which can easily be done by adding a little extra code at the end of the comparison function passed to qsort().

order(x, decreasing=TRUE) is not always equivalent to rev(order(x)).

order, sort, and rank methods for specific vector-like objects should adhere to the same underlying order that should be conceptually defined as a binary relation on the set of all possible vector values. For completeness, this binary relation should also be incarnated by a <= method.

See Also

• base::order for the default order method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• order,IntegerRanges-method in the IRanges package for an example of a specific order method (defined for IntegerRanges objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

order
showMethods("order")
selectMethod("order", "ANY")  # the default method

Description

Get or set the organism and/or species of an object.

Usage

organism(object)
organism(object) <- value

species(object)
species(object) <- value

Arguments

Value

organism should return the scientific name (i.e. genus and species, or genus and species and subspecies) of the organism. Preferably in the format "Genus species" (e.g. "Homo sapiens") or "Genus species subspecies" (e.g. "Homo sapiens neanderthalensis").

species should of course return the species of the organism. Unfortunately there is a long history of misuse of this accessor in Bioconductor so its usage is now discouraged (starting with BioC 3.1).

Note

TO DEVELOPERS:

species has been historically misused in many places in Bioconductor and is redundant with organism. So implementing the species accessor is now discouraged (starting with BioC 3.1). The organism accessor (returning the scientific name) should be implemented instead.

See Also

• http://bioconductor.org/packages/release/BiocViews.html#___Organism for browsing the annotation packages currently available in Bioconductor by organism.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• organism,character-method and organism,chromLocation-method in the annotate package for examples of specific organism methods (defined for character and chromLocation objects).

• species,AnnotationDb-method in the AnnotationDbi package for an example of a specific species method (defined for AnnotationDb objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## organism() getter:
organism
showMethods("organism")

library(annotate)
showMethods("organism")
selectMethod("organism", "character")
selectMethod("organism", "chromLocation")

## organism() setter:
`organism<-`
showMethods("organism<-")

## species() getter:
species
showMethods("species")

library(AnnotationDbi)
selectMethod("species", "AnnotationDb")

## species() setter:
`species<-`
showMethods("species<-")

Description

paste concatenates vectors of strings or vector-like objects containing strings.

NOTE: This man page is for the paste S4 generic function defined in the BiocGenerics package. See ?base::paste for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like objects containing strings) not supported by the default method.

Usage

paste(..., sep=" ", collapse=NULL, recycle0=FALSE)

Arguments

Value

See ?base::paste for the value returned by the default method.

Specific methods defined in Bioconductor packages will typically return an object of the same class as the input objects.

See Also

• base::paste for the default paste method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• paste,Rle-method in the S4Vectors package for an example of a specific paste method (defined for Rle objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

paste
showMethods("paste")
selectMethod("paste", "ANY")  # the default method

Description

paste2() is a simplified version of paste0() that takes only two arguments and follows the same rules as arithmetic operations (+, *, etc...) for recycling and propagation of names, dimensions, and dimnames.

add_prefix() and add_suffix() are simple wrappers around paste2() provided for convenience and code readability.

Usage

paste2(x, y)

add_prefix(x, prefix="")
add_suffix(x, suffix="")

Arguments

Details

Unlike paste0(), paste2() only takes two arguments: x and y. It's defined as an S4 generic that dispatches on its two arguments and with methods for ordinary vectors and arrays. Bioconductor packages can define methods for other vector-like or array-like objects that contain strings.

paste2() follows the same rules as arithmetic operations (+, *, etc...) for recycling and propagation of names, dimensions, and dimnames:

• Recycling: The longer argument "wins" i.e. the shorter argument is recycled to the length of the longer (with a warning if the length of the latter is not a multiple of the length of the former). There's one important exception to this rule: if one of the two arguments has length 0 then no recycling is performed and a zero-length vector is returned.

• Propagation of names: The longer argument also wins. If the two arguments have the same length then the names on the first argument are propagated, if any. Otherwise the names on the second argument are propagated, if any.

• Propagation of dimensions and dimnames: If x and y are both arrays, then they must be conformable i.e. have the same dimensions. In this case the result of paste2(x, y) is a also an array of same dimensions. Furthermore it will have dimnames(x) on it if dimnames(x) is not NULL, otherwise it will have dimnames(y) on it.

add_prefix(x, prefix="") and add_suffix(x, suffix="") are convenience wrappers that just do paste2(prefix, x) and paste2(x, suffix), respectively.

Value

If x and y are both vectors, a character vector parallel to the longer vector is returned.

If one of x or y is an array and the other one a vector, an array parallel to the input array is returned.

If x and y are both arrays (in which case they must be conformable), an array parallel to x and y is returned.

See Also

• base::paste0 in base R.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• paste2,DelayedArray,DelayedArray-method in the DelayedArray package for an example of a specific paste2 method (defined for DelayedArray objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## ---------------------------------------------------------------------
## The paste2() generic and methods
## ---------------------------------------------------------------------

paste2  # note the dispatch on 'x' and 'y'
showMethods("paste2")

## ---------------------------------------------------------------------
## paste0() vs paste2()
## ---------------------------------------------------------------------

## Propagation of names:
x <- c(A="foo", B="bar")
paste0(x, "XX")  # names are lost
paste2(x, "XX")  # names are propagated
paste2(x, setNames(1:6, letters[1:6]))  # longer argument "wins"

## If 'x' or 'y' has length 0:
paste0(x, character(0))  # unname(x)
paste2(x, character(0))  # character(0)

## Propagation of dimensions and dimnames:
m <- matrix(1:12, ncol=3, dimnames=list(NULL, LETTERS[1:3]))
paste0(m, letters[1:4])  # dimensions and dimnames are lost
paste2(m, letters[1:4])  # dimensions are preserved and dimnames are
                         # propagated

## ---------------------------------------------------------------------
## add_prefix() and add_suffix()
## ---------------------------------------------------------------------

m2 <- add_prefix(m, "ID")  # same as paste2("ID", m)
add_suffix(m2, ".fasta")   # same as paste2(m2, ".fasta")

Description

Get or set the path of an object.

Usage

path(object, ...)
path(object, ...) <- value

basename(path, ...)
basename(path, ...) <- value

dirname(path, ...)
dirname(path, ...) <- value

## The purpose of the following methods is to make the basename() and
## dirname() getters work out-of-the-box on any object for which the
## path() getter works.

## S4 method for signature 'ANY'
basename(path, ...)

## S4 method for signature 'ANY'
dirname(path, ...)

## The purpose of the following replacement methods is to make the
## basename() and dirname() setters work out-of-the-box on any object
## for which the path() getter and setter work.

## S4 replacement method for signature 'character'
basename(path, ...) <- value

## S4 replacement method for signature 'ANY'
basename(path, ...) <- value

## S4 replacement method for signature 'character'
dirname(path, ...) <- value

## S4 replacement method for signature 'ANY'
dirname(path, ...) <- value

Arguments

Value

A character vector for path(object), basename(path), and dirname(path). Typically of length 1 but not necessarily. Possibly with names on it for path(object).

See Also

• base::basename for the functions the basename and dirname generics are based on.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• path,RsamtoolsFile-method in the Rsamtools package for an example of a specific path method (defined for RsamtoolsFile objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## ---------------------------------------------------------------------
## GENERIC FUNCTIONS AND DEFAULT METHODS
## ---------------------------------------------------------------------

path
showMethods("path")

`path<-`
showMethods("path<-")

basename
showMethods("basename")

`basename<-`
showMethods("basename<-")

dirname
showMethods("dirname")

`dirname`
showMethods("dirname<-")


## Default basename() and dirname() getters:
selectMethod("basename", "ANY")
selectMethod("dirname", "ANY")

## Default basename() and dirname() setters:
selectMethod("basename<-", "character")
selectMethod("basename<-", "ANY")
selectMethod("dirname<-", "character")
selectMethod("dirname<-", "ANY")

## ---------------------------------------------------------------------
## OBJECTS CONTAINING PATHS
## ---------------------------------------------------------------------

## Let's define a simple class to represent objects that contain paths:
setClass("A", slots=c(stuff="ANY", path="character"))

a <- new("A", stuff=runif(5),
              path=c(one="path/to/file1", two="path/to/file2"))

## path() getter:
setMethod("path", "A", function(object) object@path)

path(a)

## Because the path() getter works on 'a', now the basename() and
## dirname() getters also work:
basename(a)
dirname(a)

## path() setter:
setReplaceMethod("path", "A",
    function(object, ..., value)
    {
        if (length(list(...)) != 0L) {
            dots <- match.call(expand.dots=FALSE)[[3L]]
            stop(BiocGenerics:::unused_arguments_msg(dots))
        }
        object@path <- value
        object
    }
)

a <- new("A", stuff=runif(5))
path(a) <- c(one="path/to/file1", two="path/to/file2")
path(a)

## Because the path() getter and setter work on 'a', now the basename()
## and dirname() setters also work:
basename(a) <- toupper(basename(a))
path(a)
dirname(a) <- "~/MyDataFiles"
path(a)

Description

A generic function which produces an MA-plot for an object containing microarray, RNA-Seq or other data.

Usage

plotMA(object, ...)

Arguments

Value

Undefined. The function exists for its side effect, producing a plot.

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.

• plotMA in the limma package for a function with the same name that is not dispatched through this generic function.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

showMethods("plotMA")

suppressWarnings(
  if(require("DESeq2"))
    example("plotMA", package="DESeq2", local=TRUE)
)

Description

A generic function which produces a PCA-plot.

Usage

plotPCA(object, ...)

Arguments

Value

Undefined. The function exists for its side effect, producing a plot.

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.

• plotPCA in the DESeq2 package for an example method that uses this generic.

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

showMethods("plotPCA")

suppressWarnings(
  if(require("DESeq2"))
    example("plotPCA", package="DESeq2", local=TRUE)
)

Description

Returns the ranks of the values in a vector-like object. Ties (i.e., equal values) and missing values can be handled in several ways.

NOTE: This man page is for the rank S4 generic function defined in the BiocGenerics package. See ?base::rank for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

rank(x, na.last=TRUE,
     ties.method=c("average", "first", "last", "random", "max", "min"),
     ...)

Arguments

Value

See ?base::rank for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

Note

TO DEVELOPERS:

See note in ?BiocGenerics::order about "stable" order.

order, sort, and rank methods for specific vector-like objects should adhere to the same underlying order that should be conceptually defined as a binary relation on the set of all possible vector values. For completeness, this binary relation should also be incarnated by a <= method.

See Also

• base::rank for the default rank method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• rank,Vector-method in the S4Vectors package for an example of a specific rank method (defined for Vector objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

rank  # note the dispatch on the 'x' arg only
showMethods("rank")
selectMethod("rank", "ANY")  # the default method

Description

relist is a generic function with a few methods in order to allow easy inversion of unlist(x).

NOTE: This man page is for the relist S4 generic function defined in the BiocGenerics package. See ?utils::relist for the default method (defined in the utils package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

relist(flesh, skeleton)

Arguments

Value

A list-like object with the same "shape" as skeleton and that would give flesh back if unlist()ed.

See Also

• utils::relist for the default relist method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• relist,ANY,List-method in the IRanges package for an example of a specific relist method (defined for when skeleton is a List object).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

relist
showMethods("relist")
selectMethod("relist", c("ANY", "ANY"))  # the default method

Description

rep.int replicates the elements in x.

NOTE: This man page is for the rep.int S4 generic function defined in the BiocGenerics package. See ?base::rep.int for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like) not supported by the default method.

Usage

rep.int(x, times)

Arguments

Value

See ?base::rep.int for the value returned by the default method.

Specific methods defined in Bioconductor packages will typically return an object of the same class as the input object.

See Also

• base::rep.int for the default rep.int method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• rep.int,Rle-method in the S4Vectors package for an example of a specific rep.int method (defined for Rle objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

rep.int
showMethods("rep.int")
selectMethod("rep.int", "ANY")  # the default method

Description

residuals is a generic function which extracts model residuals from objects returned by modeling functions.

NOTE: This man page is for the residuals S4 generic function defined in the BiocGenerics package. See ?stats::residuals for the default method (defined in the stats package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

residuals(object, ...)

Arguments

Value

Residuals extracted from the object object.

See Also

• stats::residuals for the default residuals method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• residuals,PLMset-method in the affyPLM package for an example of a specific residuals method (defined for PLMset objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

residuals
showMethods("residuals")
selectMethod("residuals", "ANY")  # the default method

Description

Get or set the row or column names of a matrix-like object.

NOTE: This man page is for the rownames, `rownames<-`, colnames, and `colnames<-` S4 generic functions defined in the BiocGenerics package. See ?base::rownames for the default methods (defined in the base package). Bioconductor packages can define specific methods for objects (typically matrix-like) not supported by the default methods.

Usage

rownames(x, do.NULL=TRUE, prefix="row")
rownames(x) <- value

colnames(x, do.NULL=TRUE, prefix="col")
colnames(x) <- value

Arguments

Value

The getters will return NULL or a character vector of length nrow(x) for rownames and length ncol(x) for colnames(x).

See ?base::rownames for more information about the default methods, including how the setters are expected to behave.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default methods.

See Also

• base::rownames for the default rownames, `rownames<-`, colnames, and `colnames<-` methods.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• rownames,DataFrame-method in the S4Vectors package for an example of a specific rownames method (defined for DataFrame objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## rownames() getter:
rownames  # note the dispatch on the 'x' arg only
showMethods("rownames")
selectMethod("rownames", "ANY")  # the default method

## rownames() setter:
`rownames<-`
showMethods("rownames<-")
selectMethod("rownames<-", "ANY")  # the default method

## colnames() getter:
colnames  # note the dispatch on the 'x' arg only
showMethods("colnames")
selectMethod("colnames", "ANY")  # the default method

## colnames() setter:
`colnames<-`
showMethods("colnames<-")
selectMethod("colnames<-", "ANY")  # the default method

Description

Some old-style (aka S3) classes are turned into formally defined (aka S4) classes by the BiocGenerics package. This allows S4 methods defined in Bioconductor packages to use them in their signatures.

Details

S3 classes currently turned into S4 classes:

• connection class and subclasses: connection, file, url, gzfile, bzfile, unz, pipe, fifo, sockconn, terminal, textConnection, gzcon. Addtitionally the character_OR_connection S4 class is defined as the union of classes character and connection.

• others: AsIs, dist

See Also

setOldClass and setClassUnion in the methods package.

Description

Generic function to write a single R object to a file.

NOTE: This man page is for the saveRDS S4 generic function and default method defined in the BiocGenerics package. See ?base::saveRDS for the corresponding function defined in base R.

Usage

saveRDS(object, file="", ascii=FALSE, version=NULL,
        compress=TRUE, refhook=NULL)

Arguments

Details

The default saveRDS method defined in this package is a thin wrapper around base::saveRDS that issues a warning if the object to serialize contains out-of-memory data. See ?containsOutOfMemoryData for more information.

Bioconductor packages can override this default method with more specialized methods.

Value

An invisible NULL.

See Also

• base::saveRDS in the base package for the default saveRDS method.

• containsOutOfMemoryData for determining whether an object contains out-of-memory data or not.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• saveRDS,SummarizedExperiment-method in the SummarizedExperiment package for an example of a specific saveRDS method (defined for SummarizedExperiment objects and derivatives).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

saveRDS  # note the dispatch on the 'object' arg only
showMethods("saveRDS")
selectMethod("saveRDS", "ANY")  # the default method

Description

Get or set the score value contained in an object.

Usage

score(x, ...)
score(x, ...) <- value

Arguments

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.

• score,GenomicRanges-method in the GenomicRanges package for an example of a specific score method (defined for GenomicRanges objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

score
showMethods("score")

`score<-`
showMethods("score<-")

library(GenomicRanges)

showMethods("score")
selectMethod("score", "GenomicRanges")

showMethods("score<-")
selectMethod("score<-", "GenomicRanges")

Description

Performs set union, intersection, (asymmetric!) difference, and equality on two or more vector-like objects.

NOTE: This man page is for the union, intersect, setdiff, and setequal S4 generic functions defined in the BiocGenerics package. See ?generics::union for the default methods (defined in CRAN package generics). Bioconductor packages can define specific methods for objects (typically vector-like) not supported by the default methods.

Usage

union(x, y, ...)
intersect(x, y, ...)
setdiff(x, y, ...)
setequal(x, y, ...)

Arguments

Value

See ?generics::union in CRAN package generics for the value returned by the default methods.

Specific methods defined in Bioconductor packages will typically act as endomorphisms, that is, they'll return an object of the same class as the input objects.

Note

The default S4 methods for these S4 generics are the union, intersect, setdiff, and setequal functions defined in CRAN package generics, which are themselves S3 generic functions. These S3 generics in turn have default methods that simply call the corresponding base R function i.e. the union, intersect, setdiff, or setequal function defined in the base package. See for example generics:::union.default.

Note that the base R functions only take 2 arguments. However, the S3 generics in CRAN package generics, and the S4 generics in BiocGenerics, add ... (a.k.a. ellipsis) to the argument list. This allow these generics to be called with an arbitrary number of effective arguments.

For union or intersect, this means that Bioconductor packages can implement N-ary union or intersection operations, that is, methods that compute the union or intersection of more than 2 objects.

However, for setdiff and setequal, which are conceptually binary-only operation, the presence of the ellipsis typically allows methods to support extra arguments to control/alter the behavior of the operation. Like for example the ignore.strand argument supported by the setdiff method for GenomicRanges objects (defined in the GenomicRanges package). (Note that the union and intersect methods for those objects also support the ignore.strand argument.)

See Also

• generics::union for the default union, intersect, setdiff, and setequal S4 methods defined in CRAN package generics.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• union,GenomicRanges,GenomicRanges-method in the GenomicRanges package for examples of specific union, intersect, and setdiff methods (defined for GenomicRanges objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## ---------------------------------------------------------------------
## union()
## ---------------------------------------------------------------------

## S4 generic:
union  # note the dispath on 'x' and 'y'

showMethods("union")

## The default S4 method is an S3 generic function defined in
## CRAN package generics:
selectMethod("union", c("ANY", "ANY"))

## The default S3 method just calls base::union():
generics:::union.default

## ---------------------------------------------------------------------
## intersect()
## ---------------------------------------------------------------------

## S4 generic:
intersect  # note the dispath on 'x' and 'y'

showMethods("intersect")

## The default S4 method is an S3 generic function defined in
## CRAN package generics:
selectMethod("intersect", c("ANY", "ANY"))

## The default S3 method just calls base::intersect():
generics:::intersect.default

## ---------------------------------------------------------------------
## setdiff()
## ---------------------------------------------------------------------

## S4 generic:
setdiff  # note the dispath on 'x' and 'y'

showMethods("setdiff")

## The default S4 method is an S3 generic function defined in
## CRAN package generics:
selectMethod("setdiff", c("ANY", "ANY"))

## The default S3 method just calls base::setdiff():
generics:::setdiff.default

## ---------------------------------------------------------------------
## setequal()
## ---------------------------------------------------------------------

## S4 generic:
setequal  # note the dispath on 'x' and 'y'

showMethods("setequal")

## The default S4 method is an S3 generic function defined in
## CRAN package generics:
selectMethod("setequal", c("ANY", "ANY"))

## The default S3 method just calls base::setequal():
generics:::setequal.default

Description

Sort a vector-like object into ascending or descending order.

NOTE: This man page is for the sort S4 generic function defined in the BiocGenerics package. See ?base::sort for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

sort(x, decreasing=FALSE, ...)

Arguments

Value

See ?base::sort for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

Note

TO DEVELOPERS:

See note in ?BiocGenerics::order about "stable" order.

order, sort, and rank methods for specific vector-like objects should adhere to the same underlying order that should be conceptually defined as a binary relation on the set of all possible vector values. For completeness, this binary relation should also be incarnated by a <= method.

See Also

• base::sort for the default sort method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• sort,Vector-method in the S4Vectors package for an example of a specific sort method (defined for Vector objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

sort  # note the dispatch on the 'x' arg only
showMethods("sort")
selectMethod("sort", "ANY")  # the default method

Description

Get or set the start, end, width, or single positions stored in an object.

NOTE: This man page is for the start, `start<-`, end, `end<-`, width, `width<-`, and pos S4 generic functions defined in the BiocGenerics package. See ?stats::start for the start and end S3 generics defined in the stats package.

Usage

start(x, ...)
start(x, ...) <- value

end(x, ...)
end(x, ...) <- value

width(x)
width(x, ...) <- value

pos(x)

Arguments

Value

See specific methods defined in Bioconductor packages.

See Also

• stats::start in the stats package for the start and end S3 generics.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• start,IRanges-method in the IRanges package for examples of specific start, end, and width methods (defined for IRanges objects).

• pos,UnstitchedIPos-method in the IRanges package for an example of a specific pos method (defined for UnstitchedIPos objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## start() getter:
start
showMethods("start")

library(IRanges)
showMethods("start")
selectMethod("start", "IRanges")  # start() getter for IRanges objects

## start() setter:
`start<-`
showMethods("start<-")
selectMethod("start<-", "IRanges")  # start() setter for IRanges objects

## end() getter:
end
showMethods("end")
selectMethod("end", "IRanges")  # end() getter for IRanges objects

## end() setter:
`end<-`
showMethods("end<-")
selectMethod("end<-", "IRanges")  # end() setter for IRanges objects

## width() getter:
width
showMethods("width")
selectMethod("width", "IRanges")  # width() getter for IRanges objects

## width() setter:
`width<-`
showMethods("width<-")
selectMethod("width<-", "IRanges")  # width() setter for IRanges objects

## pos() getter:
pos
showMethods("pos")
selectMethod("pos", "UnstitchedIPos")  # pos() getter for UnstitchedIPos
                                       # objects

Description

Get or set the strand information contained in an object.

Usage

strand(x, ...)
strand(x, ...) <- value

unstrand(x)

invertStrand(x)
## S4 method for signature 'ANY'
invertStrand(x)

Arguments

Details

All the strand methods defined in the GenomicRanges package use the same set of 3 values (called the "standard strand levels") to specify the strand of a genomic location: +, -, and *. * is used when the exact strand of the location is unknown, or irrelevant, or when the "feature" at that location belongs to both strands.

Note that unstrand is not a generic function, just a convenience wrapper to the generic strand() setter (strand<-) that does:

  strand(x) <- "*"
  x

The default method for invertStrand does:

  strand(x) <- invertStrand(strand(x))
  x

Value

If x is a vector-like object, strand(x) will typically return a vector-like object parallel to x, that is, an object of the same length as x where the i-th element describes the strand of the i-th element in x.

unstrand(x) and invertStrand(x) return a copy of x with the strand set to "*" for unstrand or inverted for invertStrand (i.e. "+" and "-" switched, and "*" untouched).

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.

• strand,GRanges-method in the GenomicRanges package for an example of a specific strand method (defined for GRanges objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

strand
showMethods("strand")

`strand<-`
showMethods("strand<-")

unstrand

invertStrand
showMethods("invertStrand")
selectMethod("invertStrand", "ANY")  # the default method

library(GenomicRanges)

showMethods("strand")
selectMethod("strand", "missing")
strand()

showMethods("strand<-")

Description

Return subsets of vector-like, matrix-like or data-frame-like objects which meet conditions.

NOTE: This man page is for the subset S4 generic function defined in the BiocGenerics package. See ?base::subset for the subset S3 generic defined in the base package.

Usage

subset(x, ...)

Arguments

Value

An object similar to x containing just the selected elements (for a vector-like object), or the selected rows and columns (for a matrix-like or data-frame-like object).

See Also

• base::subset in the base package for the subset S3 generic.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• subset,RectangularData-method in the S4Vectors package for an example of a specific subset method (defined for RectangularData derivatives).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

subset
showMethods("subset")
selectMethod("subset", "ANY")  # the default method

library(S4Vectors)
showMethods("subset")
## The subset() method for RectangularData derivatives:
selectMethod("subset", "RectangularData")

Description

Given a rectangular object x, t returns the transpose of x.

NOTE: This man page is for the t S4 generic function defined in the BiocGenerics package. See ?base::t for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically array-like) not supported by the default method.

Usage

t(x)

Arguments

Value

See ?base::t for the value returned by the default method.

Specific methods defined in Bioconductor packages will typically return an object of the same class as the input object.

See Also

• base::t for the default t method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• t,Hits-method in the S4Vectors package for an example of a specific t method (defined for Hits objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

t
showMethods("t")
selectMethod("t", "ANY")  # the default method

Description

table uses the cross-classifying factors to build a contingency table of the counts at each combination of factor levels.

NOTE: This man page is for the table S4 generic function defined in the BiocGenerics package. See ?base::table for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

table(...)

Arguments

Value

See ?base::table for the value returned by the default method.

Specific methods defined in Bioconductor packages should also return the type of object returned by the default method.

See Also

• base::table for the default table method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• table,Rle-method in the S4Vectors package for an example of a specific table method (defined for Rle objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

table
showMethods("table")
selectMethod("table", "ANY")  # the default method

Description

tapply applies a function to each cell of a ragged array, that is to each (non-empty) group of values given by a unique combination of the levels of certain factors.

NOTE: This man page is for the tapply S4 generic function defined in the BiocGenerics package. See ?base::tapply for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically list-like or vector-like) not supported by the default method.

Usage

tapply(X, INDEX, FUN=NULL, ..., default=NA, simplify=TRUE)

Arguments

Value

See ?base::tapply for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::tapply for the default tapply method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• tapply,Vector,ANY-method in the IRanges package for an example of a specific tapply method (defined for Vector objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

tapply  # note the dispatch on the 'X' and 'INDEX' args only
showMethods("tapply")
selectMethod("tapply", c("ANY", "ANY"))  # the default method

Description

testPackage helps developers implement unit tests using the RUnit testing conventions.

Usage

testPackage(pkgname=NULL, subdir="unitTests", pattern="^test_.*\\.R$",
    path=getwd())

Arguments

Details

This function is not exported from the package namespace, and must be invoked using triple colons, BiocGenerics:::testPackage(); it is provided primarily for the convenience of developers.

When invoked with missing or NULL pkgname argument, the function assumes that it has been invoked from within the package source tree (or that the source tree is located above path), and finds unit tests in subdir="unitTests" in either the base or inst/ directories at the root of the package source tree. This mode is useful when developing unit tests, since the package does not have to be re-installed to run an updated test.

When invoked with pkgname set to the name of an installed package, unit tests are searched for in the installed package directory.

Value

The function returns the result of RUnit::runTestSuite invoked on the unit tests specified in the function call.

See Also

http://bioconductor.org/developers/how-to/unitTesting-guidelines/

Examples

## Run unit tests found in the library location where
## BiocGenerics is installed
BiocGenerics:::testPackage("BiocGenerics")
## Not run: ## Run unit tests for the package whose source tree implied
## by getwd()
BiocGenerics:::testPackage()

## End(Not run)

Description

toTable() is an S4 generic function provided as an alternative to as.data.frame().

Usage

toTable(x, ...)

Arguments

Value

A data frame.

See Also

• The as.data.frame S4 generic defined in the BiocGenerics package.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• toTable,Bimap-method in the AnnotationDbi package for an example of a specific toTable method (defined for Bimap objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

toTable
showMethods("toTable")

library(AnnotationDbi)
showMethods("toTable")
selectMethod("toTable", "Bimap")

Description

Get or set the type of an object.

Note that type and type<- are defined as S4 generic functions and what type means exactly (and what type() returns) depends on the objects for which the type and/or type<- methods are defined.

Usage

type(x)
type(x) <- value

## Methods defined in the BiocGenerics package:

## S4 method for signature 'vector'
type(x)
## S4 method for signature 'array'
type(x)
## S4 method for signature 'factor'
type(x)  # returns "character"
## S4 method for signature 'data.frame'
type(x)

## S4 replacement method for signature 'vector'
type(x) <- value
## S4 replacement method for signature 'array'
type(x) <- value

Arguments

Details

On an ordinary vector, matrix, or array x, type(x) returns typeof(x).

On a data frame x where all the columns are ordinary vectors or factors, type(x) is semantically equivalent to typeof(as.matrix(x)). However, the actual implementation is careful to avoid turning the full data frame x into a matrix, as this would tend to be very inefficient in general.

Note that for a matrix-like or array-like object, type(x) returns the type of the elements in the object. See ?S4Arrays::type for more information.

Value

type(x) is expected to return the type of x as a single string i.e. as a character vector of length 1.

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.

• type,ANY-method in the S4Arrays package for the default type method.

• type,DataFrame-method in the S4Arrays package, and type,PairwiseAlignments-method in the pwalign package, for examples of specific type methods (defined for DataFrame and PairwiseAlignments objects, respectively).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

type
showMethods("type")

`type<-`
showMethods("type<-")

## The BiocGenerics package defines methods for ordinary vectors, arrays,
## and data frames:
m <- matrix(11:22, nrow=3)
type(m)           # equivalent to 'typeof(m)' or 'storage.mode(m)'
type(m) <- "raw"  # equivalent to 'storage.mode(m) <- "raw"'
m
type(m)

selectMethod("type", "array")

selectMethod("type<-", "array")

df <- data.frame(a=44:49, b=letters[1:6], c=c(TRUE, FALSE))
stopifnot(identical(type(df), typeof(as.matrix(df))))

## Examples of methods defined in other packages:

library(S4Arrays)
showMethods("type")
selectMethod("type", "ANY")  # the default "type" method

library(pwalign)
showMethods("type")
## The type() method for PairwiseAlignments objects:
selectMethod("type", "PairwiseAlignments")

Description

unique returns an object of the same class as x (typically a vector-like, data-frame-like, or array-like object) but with duplicate elements/rows removed.

NOTE: This man page is for the unique S4 generic function defined in the BiocGenerics package. See ?base::unique for the default method (defined in the base package). Bioconductor packages can define specific methods for objects (typically vector-like or data-frame-like) not supported by the default method.

Usage

unique(x, incomparables=FALSE, ...)

Arguments

Value

See ?base::unique for the value returned by the default method.

Specific methods defined in Bioconductor packages will typically return an object of the same class as the input object.

unique should always behave consistently with BiocGenerics::duplicated.

See Also

• base::unique for the default unique method.

• BiocGenerics::duplicated for determining duplicate elements.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• unique,Rle-method in the S4Vectors package for an example of a specific unique method (defined for Rle objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

unique
showMethods("unique")
selectMethod("unique", "ANY")  # the default method

Description

Given a list-like object x, unlist produces a vector-like object obtained by concatenating (conceptually thru c) all the top-level elements in x (each of them being expected to be a vector-like object, typically).

NOTE: This man page is for the unlist S4 generic function defined in the BiocGenerics package. See ?base::unlist for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

unlist(x, recursive=TRUE, use.names=TRUE)

Arguments

Value

See ?base::unlist for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::unlist for the default unlist method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• unlist,List-method in the S4Vectors package for an example of a specific unlist method (defined for List objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

unlist  # note the dispatch on the 'x' arg only
showMethods("unlist")
selectMethod("unlist", "ANY")  # the default method

Description

Given a list-like object value and grouping f, unsplit produces a vector-like object x by conceptually reversing the split operation value <- split(x, f).

NOTE: This man page is for the unsplit S4 generic function defined in the BiocGenerics package. See ?base::unsplit for the default method (defined in the base package). Bioconductor packages can define specific methods for objects not supported by the default method.

Usage

unsplit(value, f, drop=FALSE)

Arguments

Value

See ?base::unsplit for the value returned by the default method.

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default method.

See Also

• base::unsplit for the default unsplit method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• unsplit,List-method in the IRanges package for an example of a specific unsplit method (defined for List objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

unsplit  # note the dispatch on the 'value' and 'f' args only
showMethods("unsplit")
selectMethod("unsplit", "ANY")  # the default method