S4 generic functions used in Bioconductor

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Documentation for package ‘BiocGenerics’ version 0.40.0

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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
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 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
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
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

-- P --

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