# S4 generic functions for Bioconductor

## Documentation for package ‘BiocGenerics’ version 0.22.1

- DESCRIPTION file.

## Help Pages

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

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 an object into a data frame
as.vector | Coerce an object into a vector
AsIs-class | S3 classes as S4 classes

## -- B --

BiocGenerics | S4 generic functions for Bioconductor
boxplot | Box plots
bzfile-class | S3 classes as S4 classes

## -- C --

cbind | Combine objects by rows or columns
characterORconnection-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
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 | Start, end, width generic getters and setters
end<- | Start, end, width 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
lengths | Lengths of the list elements of a list-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 --

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
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
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 | Start, end, width generic getters and setters
start<- | Start, end, width 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 Transponse
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

## -- 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 | Subscript generators
which.max | Subscript generators
which.min | Subscript generators
width | Start, end, width generic getters and setters
width<- | Start, end, width generic getters and setters

## -- X --

xtabs | Cross tabulation