S4 generic functions for Bioconductor

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Documentation for package ‘BiocGenerics’ version 0.10.0

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

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
do.call Execute a function call
duplicated Determine duplicate elements

-- E --

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
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
gzcon-class S3 classes as S4 classes
gzfile-class S3 classes as S4 classes

-- I --

image Display a color image
intersect Set operations
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 --

Map Common higher-order functions in functional programming languages
mapply Apply a function to multiple list-like or vector-like arguments
match Value matching
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

-- 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
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
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
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
strand Accessing strand information
strand<- Accessing strand information

-- T --

table Cross tabulation and table creation
tapply Apply a function over a ragged array
terminal-class S3 classes as S4 classes
textConnection-class S3 classes as S4 classes

-- U --

union Set operations
unique Extract unique elements
unlist Flatten list-like objects
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

-- W --

weights Extract model weights

-- X --

xtabs Cross tabulation