BiocGenerics: S4 generic functions for Bioconductor

S4 generic functions needed by many Bioconductor packages.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BiocGenerics")
AuthorThe Bioconductor Dev Team
Bioconductor views Infrastructure
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version0.20.0

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

Functions

annotation Man page
annotation<- Man page
anyDuplicated Man page
append Man page
as.data.frame Man page
AsIs-class Man page
as.vector Man page
BiocGenerics Man page
BiocGenerics-package 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
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
Extremes Man page
fifo-class Man page
file-class Man page
fileName Man page
Filter Man page
Find Man page
funprog Man page
get Man page
getObjectSlots Man page
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
IQR Man page
is.unsorted Man page
lapply Man page
lengths Man page
mad Man page
Map Man page
mapply Man page
match Man page
mget Man page
ncol Man page
NCOL Man page
normalize Man page
nrow Man page
NROW Man page
order Man page
organism Man page
organism<- Man page
organism_species Man page
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
Position Man page
rank Man page
rbind Man page
Reduce Man page
relist Man page
rep.int Man page
residuals Man page
row+colnames Man page
rownames Man page
rownames<- Man page
S3-classes-as-S4-classes Man page
sapply Man page
score Man page
score<- Man page
setdiff Man page
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
table Man page
table-class Man page
tapply Man page
terminal-class Man page
testPackage Man page
textConnection-class Man page
union Man page
unique Man page
unlist Man page
unsplit Man page
unstrand Man page
unz-class Man page
updateObject Man page
updateObject,ANY-method Man page
updateObject,environment-method Man page
updateObject,envRefClass-method Man page
updateObject,formula-method Man page
updateObjectFromSlots Man page
updateObject,list-method Man page
url-class Man page
weights Man page
which Man page
which.max Man page
which.min Man page
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/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/table.R R/tapply.R R/testPackage.R R/unique.R R/unlist.R R/unsplit.R R/updateObject.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/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/table.Rd man/tapply.Rd man/testPackage.Rd man/unique.Rd man/unlist.Rd man/unsplit.Rd man/updateObject.Rd man/weights.Rd man/which.Rd man/xtabs.Rd
tests
tests/run_unitTests.R

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