S4 generic functions used in Bioconductor

Documentation for package ‘BiocGenerics’ version 0.36.0

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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 --

annotation	Accessing annotation information
annotation<-	Accessing annotation information
anyDuplicated	Determine duplicate elements
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
clusterApply	Apply operations using clusters
clusterApplyLB	Apply operations using clusters
clusterCall	Apply operations using clusters
clusterEvalQ	Apply operations using clusters
clusterExport	Apply operations using clusters
clusterMap	Apply operations using clusters
clusterSplit	Apply operations using clusters
colMeans	Form Row and Column Sums and Means
colnames	Row and column names
colnames<-	Row and column names
colSums	Form Row and Column Sums and Means
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
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 --

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
dims	Get the dimensions of all elements in 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
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

-- 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
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

-- O --

Ontology	Generic Ontology getter
order	Ordering permutation
organism	Organism and species accessors
organism<-	Organism and species accessors
organism_species	Organism and species accessors

-- P --

parApply	Apply operations using clusters
parCapply	Apply operations using clusters
parLapply	Apply operations using clusters
parLapplyLB	Apply operations using clusters
parRapply	Apply operations using clusters
parSapply	Apply operations using clusters
parSapplyLB	Apply operations using clusters
paste	Concatenate strings
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
plotPCA-method	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
row+colnames	Row and column names
rowMeans	Form Row and Column Sums and Means
rownames	Row and column names
rownames<-	Row and column names
rowSums	Form Row and Column Sums and Means

-- S --

S3-classes-as-S4-classes	S3 classes as S4 classes
sapply	Apply a function over a list-like or vector-like object
score	Score accessor
score<-	Score accessor
sd	Variance and Standard Deviation
setdiff	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
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()
type	Accessing the type of an object
type<-	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