R: S4 generic functions used in Bioconductor

# S4 generic functions used in Bioconductor

## Documentation for package ‘BiocGenerics’ version 0.59.7

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M N O P R S T U V W X misc

BiocGenerics-package | S4 generic functions for Bioconductor

## -- A --

add_prefix | Concatenate strings (binary form)
add_suffix | Concatenate strings (binary form)
annotation | Accessing annotation information
annotation<- | Accessing annotation information
anyDuplicated | Determine duplicate elements
aperm | Transposing an array-like object
append | Append elements to a vector-like object
as.data.frame | Coerce to a data frame
as.list | Coerce to a list
as.vector | Coerce an object into a vector
AsIs-class | S3 classes as S4 classes

## -- B --

basename | Accessing the path of an object
basename-method | Accessing the path of an object
basename<- | Accessing the path of an object
basename<--method | Accessing the path of an object
BiocGenerics | S4 generic functions for Bioconductor
boxplot | Box plots
bzfile-class | S3 classes as S4 classes

## -- C --

cbind | Combine objects by rows or columns
character_OR_connection-class | S3 classes as S4 classes
class:OutOfMemoryObject | Does an object contain out-of-memory data?
colnames | Row and column names
colnames<- | Row and column names
combine | Combining or merging different Bioconductor data structures
combine-method | Combining or merging different Bioconductor data structures
conditions | Accessors and generic functions used in the context of count datasets
conditions<- | Accessors and generic functions used in the context of count datasets
connection-class | S3 classes as S4 classes
containsOutOfMemoryData | Does an object contain out-of-memory data?
containsOutOfMemoryData-method | Does an object contain out-of-memory data?
counts | Accessors and generic functions used in the context of count datasets
counts<- | Accessors and generic functions used in the context of count datasets

## -- D --

data | Data Sets
data-method | Data Sets
dbconn | Accessing SQLite DB information
dbfile | Accessing SQLite DB information
density | Kernel density estimation
design | Accessors and generic functions used in the context of count datasets
design<- | Accessors and generic functions used in the context of count datasets
dge | Accessors and generic functions used in the context of count datasets
dims | Get the dimensions of each element of a list-like object
dirname | Accessing the path of an object
dirname-method | Accessing the path of an object
dirname<- | Accessing the path of an object
dirname<--method | Accessing the path of an object
dispTable | Accessors and generic functions used in the context of count datasets
dispTable<- | Accessors and generic functions used in the context of count datasets
dist-class | S3 classes as S4 classes
do.call | Execute a function call
duplicated | Determine duplicate elements

## -- E --

end | The start(), end(), width(), and pos() generic getters and setters
end<- | The start(), end(), width(), and pos() generic getters and setters
estimateDispersions | Accessors and generic functions used in the context of count datasets
estimateSizeFactors | Accessors and generic functions used in the context of count datasets
eval | Evaluate an (unevaluated) expression
evalq | Evaluate an (unevaluated) expression
Extremes | Maxima and minima

## -- F --

fifo-class | S3 classes as S4 classes
file-class | S3 classes as S4 classes
fileName | Accessing the file name of an object
Filter | Common higher-order functions in functional programming languages
Find | Common higher-order functions in functional programming languages
format | Format an R object for pretty printing
format.list | Format an R object for pretty printing
funprog | Common higher-order functions in functional programming languages

## -- G --

get | Return the value of a named object
getObjectSlots | Update an object to its current class definition
grep | Pattern Matching and Replacement
grepl | Pattern Matching and Replacement
gzcon-class | S3 classes as S4 classes
gzfile-class | S3 classes as S4 classes

## -- I --

image | Display a color image
intersect | Set operations
invertStrand | Accessing strand information
invertStrand-method | Accessing strand information
IQR | The Interquartile Range
is.unsorted | Test if a vector-like object is not sorted

## -- L --

lapply | Apply a function over a list-like or vector-like object
longForm | Turn object into long form

## -- M --

mad | Median Absolute Deviation
Map | Common higher-order functions in functional programming languages
mapply | Apply a function to multiple list-like or vector-like arguments
match | Value matching
mean | Arithmetic Mean
mget | Return the value of a named object

## -- N --

NCOL | The number of rows/columns of an array-like object
ncol | The number of rows/columns of an array-like object
ncols | Get the dimensions of each element of a list-like object
normalize | Normalize an object
NROW | The number of rows/columns of an array-like object
nrow | The number of rows/columns of an array-like object
nrows | Get the dimensions of each element of a list-like object

## -- O --

Ontology | Generic Ontology getter
order | Ordering permutation
organism | Organism and species accessors
organism<- | Organism and species accessors
organism_species | Organism and species accessors
OutOfMemoryObject | Does an object contain out-of-memory data?
OutOfMemoryObject-class | Does an object contain out-of-memory data?

## -- P --

paste | Concatenate strings
paste2 | Concatenate strings (binary form)
paste2-method | Concatenate strings (binary form)
path | Accessing the path of an object
path<- | Accessing the path of an object
pipe-class | S3 classes as S4 classes
plotDispEsts | Accessors and generic functions used in the context of count datasets
plotMA | MA-plot: plot differences versus averages for high-throughput data
plotMA-method | MA-plot: plot differences versus averages for high-throughput data
plotPCA | PCA-plot: Principal Component Analysis plot
pmax | Maxima and minima
pmax.int | Maxima and minima
pmin | Maxima and minima
pmin.int | Maxima and minima
pos | The start(), end(), width(), and pos() generic getters and setters
Position | Common higher-order functions in functional programming languages

## -- R --

rank | Ranks the values in a vector-like object
rbind | Combine objects by rows or columns
Reduce | Common higher-order functions in functional programming languages
relist | Re-listing an unlist()ed object
rep.int | Replicate elements of a vector-like object
residuals | Extract model residuals
rotate | Rotate an object
row+colnames | Row and column names
rownames | Row and column names
rownames<- | Row and column names

## -- S --

S3-classes-as-S4-classes | S3 classes as S4 classes
sapply | Apply a function over a list-like or vector-like object
saveRDS | The saveRDS() S4 generic and default method
saveRDS-method | The saveRDS() S4 generic and default method
scale | Scaling and centering of matrix-like objects
score | Score accessor
score<- | Score accessor
sd | Variance and Standard Deviation
sequence | Create a vector of sequences
setdiff | Set operations
setequal | Set operations
setops | Set operations
sets | Set operations
sizeFactors | Accessors and generic functions used in the context of count datasets
sizeFactors<- | Accessors and generic functions used in the context of count datasets
sockconn-class | S3 classes as S4 classes
sort | Sorting a vector-like object
species | Organism and species accessors
species<- | Organism and species accessors
start | The start(), end(), width(), and pos() generic getters and setters
start<- | The start(), end(), width(), and pos() generic getters and setters
strand | Accessing strand information
strand<- | Accessing strand information
subset | Subsetting vector-like, matrix-like and data-frame-like objects

## -- T --

t | Matrix Transpose
table | Cross tabulation and table creation
table-method | Cross tabulation and table creation
tapply | Apply a function over a ragged array
terminal-class | S3 classes as S4 classes
testPackage | Run RUnit package unit tests
textConnection-class | S3 classes as S4 classes
toTable | An alternative to as.data.frame()
transform | Transform an object
type | Accessing the type of an object
type-method | Accessing the type of an object
type<- | Accessing the type of an object
type<--method | Accessing the type of an object

## -- U --

union | Set operations
unique | Extract unique elements
unlist | Flatten list-like objects
unsplit | Unsplit a list-like object
unstrand | Accessing strand information
unz-class | S3 classes as S4 classes
updateObject | Update an object to its current class definition
updateObject-method | Update an object to its current class definition
updateObjectFromSlots | Update an object to its current class definition
url-class | S3 classes as S4 classes

## -- V --

var | Variance and Standard Deviation

## -- W --

weights | Extract model weights
which | Which values in an object are considered TRUE?
which.max | What's the index of the first min or max value in an object?
which.min | What's the index of the first min or max value in an object?
width | The start(), end(), width(), and pos() generic getters and setters
width<- | The start(), end(), width(), and pos() generic getters and setters

## -- X --

xtabs | Cross tabulation

## -- misc --

%in% | Value matching