BiocGenerics: S4 generic functions for Bioconductor

S4 generic functions needed by many Bioconductor packages.

Author
The Bioconductor Dev Team
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
0.20.0

View on Bioconductor

Man pages

annotation
Accessing annotation information
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
BiocGenerics-package
S4 generic functions for Bioconductor
boxplot
Box plots
cbind
Combine objects by rows or columns
clusterApply
Apply operations using clusters
combine
Combining or merging different Bioconductor data structures
dbconn
Accessing SQLite DB information
density
Kernel density estimation
dge
Accessors and generic functions used in the context of count...
do.call
Execute a function call
duplicated
Determine duplicate elements
eval
Evaluate an (unevaluated) expression
evalq
Evaluate an (unevaluated) expression
Extremes
Maxima and minima
fileName
Accessing the file name of an object
funprog
Common higher-order functions in functional programming...
get
Return the value of a named object
grep
Pattern Matching and Replacement
image
Display a color image
IQR
The Interquartile Range
is.unsorted
Test if a vector-like object is not sorted
lapply
Apply a function over a list-like or vector-like object
lengths
Lengths of the list elements of a list-like object
mad
Median Absolute Deviation
mapply
Apply a function to multiple list-like or vector-like...
match
Value matching
normalize
Normalize an object
nrow
The number of rows/columns of an array-like object
order
Ordering permutation
organism_species
Organism and species accessors
paste
Concatenate strings
plotMA
MA-plot: plot differences versus averages for high-throughput...
plotPCA
PCA-plot: Principal Component Analysis plot
rank
Ranks the values in a vector-like object
relist
Re-listing an unlist()ed object
rep
Replicate elements of a vector-like object
residuals
Extract model residuals
row_colnames
Row and column names
S3-classes-as-S4-classes
S3 classes as S4 classes
score
Score accessor
sets
Set operations
sort
Sorting a vector-like object
start
Start, end, width generic getters and setters
strand
Accessing strand information
subset
Subsetting vector-like, matrix-like and data-frame-like...
table
Cross tabulation and table creation
tapply
Apply a function over a ragged array
testPackage
Run RUnit package unit tests
unique
Extract unique elements
unlist
Flatten list-like objects
unsplit
Unsplit a list-like object
updateObject
Update an object to its current class definition
weights
Extract model weights
which
Subscript generators
xtabs
Cross tabulation

Files in this package

BiocGenerics/DESCRIPTION
BiocGenerics/NAMESPACE
BiocGenerics/R
BiocGenerics/R/Extremes.R
BiocGenerics/R/IQR.R
BiocGenerics/R/S3-classes-as-S4-classes.R
BiocGenerics/R/annotation.R
BiocGenerics/R/append.R
BiocGenerics/R/as.data.frame.R
BiocGenerics/R/as.list.R
BiocGenerics/R/as.vector.R
BiocGenerics/R/boxplot.R
BiocGenerics/R/cbind.R
BiocGenerics/R/clusterApply.R
BiocGenerics/R/combine.R
BiocGenerics/R/dbconn.R
BiocGenerics/R/density.R
BiocGenerics/R/dge.R
BiocGenerics/R/do.call.R
BiocGenerics/R/duplicated.R
BiocGenerics/R/eval.R
BiocGenerics/R/fileName.R
BiocGenerics/R/funprog.R
BiocGenerics/R/get.R
BiocGenerics/R/grep.R
BiocGenerics/R/image.R
BiocGenerics/R/is.unsorted.R
BiocGenerics/R/lapply.R
BiocGenerics/R/lengths.R
BiocGenerics/R/mad.R
BiocGenerics/R/mapply.R
BiocGenerics/R/match.R
BiocGenerics/R/normalize.R
BiocGenerics/R/normarg-utils.R
BiocGenerics/R/nrow.R
BiocGenerics/R/order.R
BiocGenerics/R/organism_species.R
BiocGenerics/R/paste.R
BiocGenerics/R/plotMA.R
BiocGenerics/R/plotPCA.R
BiocGenerics/R/rank.R
BiocGenerics/R/relist.R
BiocGenerics/R/rep.R
BiocGenerics/R/replaceSlots.R
BiocGenerics/R/residuals.R
BiocGenerics/R/row_colnames.R
BiocGenerics/R/score.R
BiocGenerics/R/sets.R
BiocGenerics/R/sort.R
BiocGenerics/R/start.R
BiocGenerics/R/strand.R
BiocGenerics/R/subset.R
BiocGenerics/R/table.R
BiocGenerics/R/tapply.R
BiocGenerics/R/testPackage.R
BiocGenerics/R/unique.R
BiocGenerics/R/unlist.R
BiocGenerics/R/unsplit.R
BiocGenerics/R/updateObject.R
BiocGenerics/R/weights.R
BiocGenerics/R/which.R
BiocGenerics/R/xtabs.R
BiocGenerics/R/zzz.R
BiocGenerics/TODO
BiocGenerics/inst
BiocGenerics/inst/CITATION
BiocGenerics/inst/unitTests
BiocGenerics/inst/unitTests/test_combine.R
BiocGenerics/inst/unitTests/test_updateObject.R
BiocGenerics/man
BiocGenerics/man/BiocGenerics-package.Rd
BiocGenerics/man/Extremes.Rd
BiocGenerics/man/IQR.Rd
BiocGenerics/man/S3-classes-as-S4-classes.Rd
BiocGenerics/man/annotation.Rd
BiocGenerics/man/append.Rd
BiocGenerics/man/as.data.frame.Rd
BiocGenerics/man/as.vector.Rd
BiocGenerics/man/boxplot.Rd
BiocGenerics/man/cbind.Rd
BiocGenerics/man/clusterApply.Rd
BiocGenerics/man/combine.Rd
BiocGenerics/man/dbconn.Rd
BiocGenerics/man/density.Rd
BiocGenerics/man/dge.Rd
BiocGenerics/man/do.call.Rd
BiocGenerics/man/duplicated.Rd
BiocGenerics/man/eval.Rd
BiocGenerics/man/evalq.Rd
BiocGenerics/man/fileName.Rd
BiocGenerics/man/funprog.Rd
BiocGenerics/man/get.Rd
BiocGenerics/man/grep.Rd
BiocGenerics/man/image.Rd
BiocGenerics/man/is.unsorted.Rd
BiocGenerics/man/lapply.Rd
BiocGenerics/man/lengths.Rd
BiocGenerics/man/mad.Rd
BiocGenerics/man/mapply.Rd
BiocGenerics/man/match.Rd
BiocGenerics/man/normalize.Rd
BiocGenerics/man/nrow.Rd
BiocGenerics/man/order.Rd
BiocGenerics/man/organism_species.Rd
BiocGenerics/man/paste.Rd
BiocGenerics/man/plotMA.Rd
BiocGenerics/man/plotPCA.Rd
BiocGenerics/man/rank.Rd
BiocGenerics/man/relist.Rd
BiocGenerics/man/rep.Rd
BiocGenerics/man/residuals.Rd
BiocGenerics/man/row_colnames.Rd
BiocGenerics/man/score.Rd
BiocGenerics/man/sets.Rd
BiocGenerics/man/sort.Rd
BiocGenerics/man/start.Rd
BiocGenerics/man/strand.Rd
BiocGenerics/man/subset.Rd
BiocGenerics/man/table.Rd
BiocGenerics/man/tapply.Rd
BiocGenerics/man/testPackage.Rd
BiocGenerics/man/unique.Rd
BiocGenerics/man/unlist.Rd
BiocGenerics/man/unsplit.Rd
BiocGenerics/man/updateObject.Rd
BiocGenerics/man/weights.Rd
BiocGenerics/man/which.Rd
BiocGenerics/man/xtabs.Rd
BiocGenerics/tests
BiocGenerics/tests/run_unitTests.R