BiocGenerics: S4 generic functions for Bioconductor
Version 0.22.0

S4 generic functions needed by many Bioconductor packages.

Browse man pages Browse package API and functions Browse package files

AuthorThe Bioconductor Dev Team
Bioconductor views Infrastructure
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version0.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BiocGenerics")

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
matrix-summary: Form Row and Column Sums and Means
mean: Arithmetic Mean
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...
t: Matrix Transponse
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
var: Variance and Standard Deviation
weights: Extract model weights
which: Subscript generators
xtabs: Cross tabulation

Functions

AsIs-class Man page
BiocGenerics Man page
BiocGenerics-package Man page
Extremes Man page
Filter Man page
Find Man page
IQR Man page
Map Man page
NCOL Man page
NROW Man page
Position Man page
Reduce Man page
S3-classes-as-S4-classes Man page
annotation Man page
annotation<- Man page
anyDuplicated Man page
append Man page
as.data.frame Man page
as.vector Man page
boxplot Man page
bzfile-class Man page
cbind Man page
characterORconnection-class Man page
clusterApply Man page
clusterApplyLB Man page
clusterCall Man page
clusterEvalQ Man page
clusterExport Man page
clusterMap Man page
clusterSplit Man page
colMeans Man page
colSums Man page
colnames Man page
colnames<- Man page
combine Man page
combine,ANY,missing-method Man page
combine,data.frame,data.frame-method Man page
combine,matrix,matrix-method Man page
conditions Man page
conditions<- Man page
connection-class Man page
counts Man page
counts<- Man page
dbconn Man page
dbfile Man page
density Man page
design Man page
design<- Man page
dispTable Man page
dispTable<- Man page
dist-class Man page
do.call Man page
duplicated Man page
end Man page
end<- Man page
estimateDispersions Man page
estimateSizeFactors Man page
eval Man page
evalq Man page Source code
extraArgsAsList Source code
fifo-class Man page
file-class Man page
fileName Man page
funprog Man page
get Man page
getObjectFields Source code
getObjectSlots Man page Source code
grep Man page
grepl Man page
gzcon-class Man page
gzfile-class Man page
image Man page
intersect Man page
invertStrand Man page
invertStrand,ANY-method Man page
is.unsorted Man page
isTRUEorFALSE Source code
lapply Man page
lengths Man page
mad Man page
mapply Man page
match Man page
match.useAsDefault Source code
mean Man page
mget Man page
ncol Man page
normalize Man page
nrow Man page
ntersect.useAsDefault Source code
order Man page
organism Man page
organism<- Man page
organism_species Man page
packageInfo Source code
packageRoot Source code
parApply Man page
parCapply Man page
parLapply Man page
parLapplyLB Man page
parRapply Man page
parSapply Man page
parSapplyLB Man page
paste Man page
pipe-class Man page
plotDispEsts Man page
plotMA Man page
plotMA,ANY-method Man page
plotPCA Man page
plotPCA,ANY-method Man page
pmax Man page
pmax.int Man page
pmin Man page
pmin.int Man page
rank Man page
rbind Man page
relist Man page
rep.int Man page
replaceSlots Source code
residuals Man page
row+colnames Man page
rowMeans Man page
rowSums Man page
rownames Man page
rownames<- Man page
s.rank.useAsDefault Source code
s.unsorted.useAsDefault Source code
sapply Man page
score Man page
score<- Man page
sd Man page
setdiff Man page
setdiff.useAsDefault Source code
sets Man page
sizeFactors Man page
sizeFactors<- Man page
sockconn-class Man page
sort Man page
species Man page
species<- Man page
start Man page
start<- Man page
strand Man page
strand<- Man page
subset Man page
t Man page
table Man page
table-class Man page
table.useAsDefault Source code
tapply Man page
terminal-class Man page
test Source code
testPackage Man page Source code
textConnection-class Man page
union Man page
union.useAsDefault Source code
unique Man page
unlist Man page
unsafe_replaceSlots Source code
unsplit Man page
unstrand Man page Source code
unz-class Man page
updateObject Man page
updateObject,ANY-method Man page
updateObject,envRefClass-method Man page
updateObject,environment-method Man page
updateObject,formula-method Man page
updateObject,list-method Man page
updateObjectFromFields Source code
updateObjectFromSlots Man page Source code
updateObjectFrom_errf Source code
updateS4 Source code
url-class Man page
var Man page
weights Man page
which Man page
which.max Man page
which.max.useAsDefault Source code
which.min Man page
which.min.useAsDefault Source code
which.useAsDefault Source code
width Man page
width<- Man page
xtabs Man page
xtabs-class Man page

Files

DESCRIPTION
NAMESPACE
R
R/Extremes.R
R/IQR.R
R/S3-classes-as-S4-classes.R
R/annotation.R
R/append.R
R/as.data.frame.R
R/as.list.R
R/as.vector.R
R/boxplot.R
R/cbind.R
R/clusterApply.R
R/combine.R
R/dbconn.R
R/density.R
R/dge.R
R/do.call.R
R/duplicated.R
R/eval.R
R/fileName.R
R/funprog.R
R/get.R
R/grep.R
R/image.R
R/is.unsorted.R
R/lapply.R
R/lengths.R
R/mad.R
R/mapply.R
R/match.R
R/matrix-summary.R
R/mean.R
R/normalize.R
R/normarg-utils.R
R/nrow.R
R/order.R
R/organism_species.R
R/paste.R
R/plotMA.R
R/plotPCA.R
R/rank.R
R/relist.R
R/rep.R
R/replaceSlots.R
R/residuals.R
R/row_colnames.R
R/score.R
R/sets.R
R/sort.R
R/start.R
R/strand.R
R/subset.R
R/t.R
R/table.R
R/tapply.R
R/testPackage.R
R/unique.R
R/unlist.R
R/unsplit.R
R/updateObject.R
R/var.R
R/weights.R
R/which.R
R/xtabs.R
R/zzz.R
TODO
inst
inst/CITATION
inst/unitTests
inst/unitTests/test_combine.R
inst/unitTests/test_updateObject.R
man
man/BiocGenerics-package.Rd
man/Extremes.Rd
man/IQR.Rd
man/S3-classes-as-S4-classes.Rd
man/annotation.Rd
man/append.Rd
man/as.data.frame.Rd
man/as.vector.Rd
man/boxplot.Rd
man/cbind.Rd
man/clusterApply.Rd
man/combine.Rd
man/dbconn.Rd
man/density.Rd
man/dge.Rd
man/do.call.Rd
man/duplicated.Rd
man/eval.Rd
man/evalq.Rd
man/fileName.Rd
man/funprog.Rd
man/get.Rd
man/grep.Rd
man/image.Rd
man/is.unsorted.Rd
man/lapply.Rd
man/lengths.Rd
man/mad.Rd
man/mapply.Rd
man/match.Rd
man/matrix-summary.Rd
man/mean.Rd
man/normalize.Rd
man/nrow.Rd
man/order.Rd
man/organism_species.Rd
man/paste.Rd
man/plotMA.Rd
man/plotPCA.Rd
man/rank.Rd
man/relist.Rd
man/rep.Rd
man/residuals.Rd
man/row_colnames.Rd
man/score.Rd
man/sets.Rd
man/sort.Rd
man/start.Rd
man/strand.Rd
man/subset.Rd
man/t.Rd
man/table.Rd
man/tapply.Rd
man/testPackage.Rd
man/unique.Rd
man/unlist.Rd
man/unsplit.Rd
man/updateObject.Rd
man/var.Rd
man/weights.Rd
man/which.Rd
man/xtabs.Rd
tests
tests/run_unitTests.R
BiocGenerics documentation built on May 20, 2017, 9:53 p.m.