# Biobase: Base functions for Bioconductor

## Documentation for package ‘Biobase’ version 2.2.2

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E F G H I L M N O P R S T U V W misc

## -- --

Biobase-package | Biobase Package Overview

## -- --

$,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
$,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
$<-,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
$<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
$<-,Versions-method | Class "Versions"

## -- A --

aaMap | Dataset: Names and Characteristics of Amino Acids
abstract | Retrieve Meta-data from eSets and ExpressionSets.
abstract,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
abstract,MIAME-method | Class for Storing Microarray Experiment Information
addVigs2WinMenu | Add Menu Items to an Existing/New Menu of Window
aggenv,aggregator-method | A Simple Class for Aggregators
aggfun,aggregator-method | A Simple Class for Aggregators
Aggregate | A Simple Aggregation Mechanism.
aggregator | A Simple Class for Aggregators
aggregator-class | A Simple Class for Aggregators
AnnotatedDataFrame | Class Containing Measured Variables and Their Meta-Data Description.
AnnotatedDataFrame-class | Class Containing Measured Variables and Their Meta-Data Description.
annotatedDataFrameFrom | Methods for Function annotatedDataFrameFrom in Package ‘Biobase’
annotatedDataFrameFrom,AssayData-method | Methods for Function annotatedDataFrameFrom in Package ‘Biobase’
annotatedDataFrameFrom,matrix-method | Methods for Function annotatedDataFrameFrom in Package ‘Biobase’
annotatedDataFrameFrom,NULL-method | Methods for Function annotatedDataFrameFrom in Package ‘Biobase’
annotation | Annotate eSet data.
annotation,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
annotation<-,eSet,character-method | Class to Contain High-Throughput Assays and Experimental Metadata
anyMissing | Checks if there are any missing values in an object or not
as.data.frame.ExpressionSet | Class to Contain and Describe High-Throughput Expression Level Assays.
AssayData | Class "AssayData"
assayData | Retrieve assay data from eSets and ExpressionSets.
assayData,AssayData-method | Class "AssayData"
assayData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
AssayData-class | Class "AssayData"
assayData<-,eSet,AssayData-method | Class to Contain High-Throughput Assays and Experimental Metadata
assayDataElement | Class to Contain High-Throughput Assays and Experimental Metadata
assayDataElementNames | Class to Contain High-Throughput Assays and Experimental Metadata
assayDataElementReplace | Class to Contain High-Throughput Assays and Experimental Metadata
assayDataNew | Class "AssayData"
assayDataValidMembers | Class "AssayData"

## -- B --

Biobase | Biobase Package Overview
biocReposList | Return a list of Bioconductor package repositories

## -- C --

cache | Evaluate an expression if its value is not already cached.
channel | Create a new ExpressionSet instance by selecting a specific channel
channel,NChannelSet,character-method | Class to contain data from multiple channel array technologies
channelNames | Retrieve channel names from object
channelNames,NChannelSet-method | Class to contain data from multiple channel array technologies
characterORMIAME-class | Class to Make Older Versions Compatible
class.NChannelSet | Class to contain data from multiple channel array technologies
class:aggregator | A Simple Class for Aggregators
class:AnnotatedDataFrame | Class Containing Measured Variables and Their Meta-Data Description.
class:characterORMIAME | Class to Make Older Versions Compatible
class:container | A Lockable List Structure with Constraints on Content
class:eSet | Class to Contain High-Throughput Assays and Experimental Metadata
class:ExpressionSet | Class to Contain and Describe High-Throughput Expression Level Assays.
class:MIAME | Class for Storing Microarray Experiment Information
class:MultiSet | Class to Contain and Describe High-Throughput Expression Level Assays.
class:SnpSet | Class to Contain Objects Describing High-Throughput SNP Assays.
classVersion | Retrieve information about versioned classes
classVersion,ANY-method | Retrieve information about versioned classes
classVersion,character-method | Retrieve information about versioned classes
classVersion,Versioned-method | Class "Versioned"
classVersion<-,Versioned,Versions-method | Class "Versioned"
coerce,data.frame,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
coerce,eSet,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
coerce,eSet,MultiSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
coerce,ExpressionSet,data.frame-method | Class to Contain and Describe High-Throughput Expression Level Assays.
coerce,exprSet,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
coerce,phenoData,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
coerce,Versions,character-method | Class "Versions"
combine | Methods for Function combine in Package ‘Biobase’
combine,AnnotatedDataFrame,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
combine,ANY,missing-method | Methods for Function combine in Package ‘Biobase’
combine,AssayData,AssayData-method | Class "AssayData"
combine,data.frame,data.frame-method | Methods for Function combine in Package ‘Biobase’
combine,eSet,ANY-method | Class to Contain High-Throughput Assays and Experimental Metadata
combine,eSet,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
combine,matrix,matrix-method | Methods for Function combine in Package ‘Biobase’
combine,MIAME,MIAME-method | Class for Storing Microarray Experiment Information
Compare,character,Versions-method | Class "Versions"
Compare,Versions,character-method | Class "Versions"
Compare,Versions,Versions-method | Class "Versions"
container | A Lockable List Structure with Constraints on Content
container-class | A Lockable List Structure with Constraints on Content
content,container-method | A Lockable List Structure with Constraints on Content
contents | Function to retrieve contents of environments
copyEnv | List-Environment interactions
copySubstitute | Copy Between Connections or Files with Configure-Like Name-Value Substitution
createPackage | Create a Package Directory from a Template

## -- D --

data:aaMap | Dataset: Names and Characteristics of Amino Acids
data:geneCov | Sample expression matrix and phenotype data.frames.
data:geneCovariate | Sample expression matrix and phenotype data.frames.
data:geneData | Sample expression matrix and phenotype data.frames.
data:reporter | Example data.frame representing reporter information
data:sample.ExpressionSet | Dataset of class 'ExpressionSet'
data:sample.MultiSet | Data set of class 'MultiSet'
data:seD | Sample expression matrix and phenotype data.frames.
description | Retrieve and set overall experimental information eSet-like classes.
description,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
description<-,eSet,MIAME-method | Class to Contain High-Throughput Assays and Experimental Metadata
dim,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
dim,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
dimLabels | Class Containing Measured Variables and Their Meta-Data Description.
dimLabels,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
dimLabels<-,AnnotatedDataFrame,character-method | Class Containing Measured Variables and Their Meta-Data Description.
dims | Retrieve dimensions of all elements in a list or environment
dims,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
dumpPackTxt | Dump Textual Description of a Package

## -- E --

esApply | An apply-like function for ExpressionSet and related structures.
esApply,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
eSet | Class to Contain High-Throughput Assays and Experimental Metadata
eSet-class | Class to Contain High-Throughput Assays and Experimental Metadata
experimentData | Retrieve Meta-data from eSets and ExpressionSets.
experimentData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
experimentData<-,eSet,MIAME-method | Class to Contain High-Throughput Assays and Experimental Metadata
expinfo,MIAME-method | Class for Storing Microarray Experiment Information
ExpressionSet | Class to Contain and Describe High-Throughput Expression Level Assays.
ExpressionSet-class | Class to Contain and Describe High-Throughput Expression Level Assays.
exprs | Retrieve expression data from eSets.
exprs,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
exprs,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
exprs,SnpSet-method | Class to Contain Objects Describing High-Throughput SNP Assays.
exprs<-,eSet,AssayData-method | Class to Contain High-Throughput Assays and Experimental Metadata
exprs<-,ExpressionSet,matrix-method | Class to Contain and Describe High-Throughput Expression Level Assays.
exprs<-,SnpSet,matrix-method | Class to Contain Objects Describing High-Throughput SNP Assays.

## -- F --

fData | Retrieve information on features recorded in eSet-derived classes.
fData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
fData<-,eSet,data.frame-method | Class to Contain High-Throughput Assays and Experimental Metadata
featureData | Retrieve information on features recorded in eSet-derived classes.
featureData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
featureData<-,eSet,AnnotatedDataFrame-method | Class to Contain High-Throughput Assays and Experimental Metadata
featureNames | Retrieve feature and sample names from eSets.
featureNames,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
featureNames,AssayData-method | Class "AssayData"
featureNames,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
featureNames<-,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
featureNames<-,AssayData-method | Class "AssayData"
featureNames<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
fvarLabels | Retrieve information on features recorded in eSet-derived classes.
fvarLabels,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
fvarLabels<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
fvarMetadata | Retrieve information on features recorded in eSet-derived classes.
fvarMetadata,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
fvarMetadata<-,eSet,data.frame-method | Class to Contain High-Throughput Assays and Experimental Metadata

## -- G --

geneCov | Sample expression matrix and phenotype data.frames.
geneCovariate | Sample expression matrix and phenotype data.frames.
geneData | Sample expression matrix and phenotype data.frames.
getObjectSlots | Update an object to its current class definition
getPkgVigs | List Vignette Files for a Package

## -- H --

hybridizations,MIAME-method | Class for Storing Microarray Experiment Information

## -- I --

initfun,aggregator-method | A Simple Class for Aggregators
initialize,aggregator-method | A Simple Class for Aggregators
initialize,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
initialize,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
initialize,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
initialize,MultiSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
initialize,NChannelSet-method | Class to contain data from multiple channel array technologies
initialize,SnpSet-method | Class to Contain Objects Describing High-Throughput SNP Assays.
initialize,Versioned-method | Class "Versioned"
initialize,Versions-method | Class "Versions"
initialize,VersionsNull-method | Class "VersionsNull"
isCurrent | Use version information to test whether class is current
isCurrent,ANY,ANY-method | Use version information to test whether class is current
isCurrent,MIAME,missing-method | Class for Storing Microarray Experiment Information
isCurrent,Versioned,character-method | Class "Versioned"
isCurrent,Versioned,missing-method | Class "Versioned"
isUnique | Determine Unique Elements
isVersioned | Determine whether object or class contains versioning information
isVersioned,ANY-method | Determine whether object or class contains versioning information
isVersioned,character-method | Determine whether object or class contains versioning information
isVersioned,Versioned-method | Class "Versioned"

## -- L --

l2e | List-Environment interactions
lcPrefix | Compute the longest common prefix or suffix of a string
lcPrefixC | Compute the longest common prefix or suffix of a string
lcSuffix | Compute the longest common prefix or suffix of a string
length,container-method | A Lockable List Structure with Constraints on Content
listLen | Lengths of list elements
listOrEnv | Class to Contain High-Throughput Assays and Experimental Metadata
locked,container-method | A Lockable List Structure with Constraints on Content

## -- M --

makeDataPackage | Make an R package from a data object
makeDataPackage,ANY-method | Make an R package from a data object
makeDataPackage,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
matchpt | Nearest neighbor search.
MIAME | Class for Storing Microarray Experiment Information
MIAME-class | Class for Storing Microarray Experiment Information
mkScalar | Utility classes for length one (scalar) objects
multiassign | Assign Values to a Names
MultiSet | Class to Contain and Describe High-Throughput Expression Level Assays.
MultiSet-class | Class to Contain and Describe High-Throughput Expression Level Assays.

## -- N --

NChannelSet | Class to contain data from multiple channel array technologies
NChannelSet-class | Class to contain data from multiple channel array technologies
ncol,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
ncol,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
normControls,MIAME-method | Class for Storing Microarray Experiment Information
note | Informational Messages
notes | Retrieve and set eSet notes.
notes,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
notes,MIAME-method | Class for Storing Microarray Experiment Information
notes<-,eSet,ANY-method | Class to Contain High-Throughput Assays and Experimental Metadata
notes<-,MIAME,character-method | Class for Storing Microarray Experiment Information
notes<-,MIAME,list-method | Class for Storing Microarray Experiment Information

## -- O --

openPDF | Open PDF Files in a Standard Viewer
openVignette | Open a Vignette or Show Vignette Selection Menu
otherInfo,MIAME-method | Class for Storing Microarray Experiment Information

## -- P --

package.version | Report Version of a Package
pData | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
pData,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
pData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
pData<-,AnnotatedDataFrame,data.frame-method | Class Containing Measured Variables and Their Meta-Data Description.
pData<-,eSet,data.frame-method | Class to Contain High-Throughput Assays and Experimental Metadata
phenoData | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
phenoData,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
phenoData<-,eSet,AnnotatedDataFrame-method | Class to Contain High-Throughput Assays and Experimental Metadata
preproc | Class for Storing Microarray Experiment Information
preproc,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
preproc,MIAME-method | Class for Storing Microarray Experiment Information
preproc<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
preproc<-,MIAME-method | Class for Storing Microarray Experiment Information
pubMedIds | Retrieve Meta-data from eSets and ExpressionSets.
pubMedIds,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
pubMedIds,MIAME-method | Class for Storing Microarray Experiment Information
pubMedIds<-,eSet,character-method | Class to Contain High-Throughput Assays and Experimental Metadata
pubMedIds<-,MIAME,ANY-method | Class for Storing Microarray Experiment Information

## -- R --

read.AnnotatedDataFrame | Read 'AnnotatedDataFrame'
read.MIAME | Read MIAME Information into an Instance of Class 'MIAME'
readExpressionSet | Read 'ExpressionSet'
reporter | Example data.frame representing reporter information
reverseSplit | A function to reverse the role of names and values in a list.
rowMax | A function to compute empirical row quantiles.
rowMedians | Calculates the median for each row in a matrix
rowMedians,ExpressionSet-method | Calculates the median for each row in a matrix
rowMedians,matrix-method | Calculates the median for each row in a matrix
rowMin | A function to compute empirical row quantiles.
rowQ | A function to compute empirical row quantiles.
rowQ,ExpressionSet,numeric-method | A function to compute empirical row quantiles.
rowQ,matrix,numeric-method | A function to compute empirical row quantiles.

## -- S --

sample.ExpressionSet | Dataset of class 'ExpressionSet'
sample.MultiSet | Data set of class 'MultiSet'
sampleNames | Retrieve feature and sample names from eSets.
sampleNames,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
sampleNames,AssayData-method | Class "AssayData"
sampleNames,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
sampleNames,NChannelSet-method | Class to contain data from multiple channel array technologies
sampleNames<-,AnnotatedDataFrame,ANY-method | Class Containing Measured Variables and Their Meta-Data Description.
sampleNames<-,AssayData,ANY-method | Class "AssayData"
sampleNames<-,AssayData,list-method | Class "AssayData"
sampleNames<-,eSet,ANY-method | Class to Contain High-Throughput Assays and Experimental Metadata
sampleNames<-,NChannelSet,list-method | Class to contain data from multiple channel array technologies
samples | Class for Storing Microarray Experiment Information
samples,MIAME-method | Class for Storing Microarray Experiment Information
ScalarCharacter-class | Utility classes for length one (scalar) objects
ScalarInteger-class | Utility classes for length one (scalar) objects
ScalarNumeric-class | Utility classes for length one (scalar) objects
ScalarObject-class | Utility classes for length one (scalar) objects
se.exprs | Retrieve expression data from eSets.
se.exprs<- | Retrieve expression data from eSets.
seD | Sample expression matrix and phenotype data.frames.
selectChannels | Create a new NChannelSet instance by selecting specific channels
selectChannels,NChannelSet,character-method | Class to contain data from multiple channel array technologies
selectSome | Extract elements of a vector for concise rendering
show,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
show,container-method | A Lockable List Structure with Constraints on Content
show,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
show,MIAME-method | Class for Storing Microarray Experiment Information
show,ScalarCharacter-method | Utility classes for length one (scalar) objects
show,ScalarObject-method | Utility classes for length one (scalar) objects
show,Versioned-method | Class "Versioned"
show,Versions-method | Class "Versions"
show,VersionsNull-method | Class "VersionsNull"
SnpSet | Class to Contain Objects Describing High-Throughput SNP Assays.
SnpSet-class | Class to Contain Objects Describing High-Throughput SNP Assays.
storageMode | Retrieve or set storage mode for eSets.
storageMode,AssayData-method | Class "AssayData"
storageMode,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
storageMode<-,AssayData,character-method | Class "AssayData"
storageMode<-,eSet,character-method | Class to Contain High-Throughput Assays and Experimental Metadata
strbreak | Break Character Strings to Fit Width
subListExtract | Extract the same element from the sublists of a list
SW | Class to Contain High-Throughput Assays and Experimental Metadata

## -- T --

testBioCConnection | A function to check internet connectivity to Bioconductor

## -- U --

updateObject | Update an object to its current class definition
updateObject,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
updateObject,ANY-method | Update an object to its current class definition
updateObject,environment-method | Update an object to its current class definition
updateObject,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
updateObject,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
updateObject,list-method | Update an object to its current class definition
updateObject,MIAME-method | Class for Storing Microarray Experiment Information
updateObject,Versions-method | Class "Versions"
updateObjectFromSlots | Update an object to its current class definition
updateObjectTo | Update an object to its current class definition
updateObjectTo,ANY,ANY-method | Update an object to its current class definition
updateObjectTo,eSet,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
updateOldESet | Update previously created eSet object to current eSet structure
userQuery | A function to query the user for input

## -- V --

validMsg | Conditionally append result to validity message
varLabels | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
varLabels,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
varLabels,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
varLabels<-,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
varLabels<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
varMetadata | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
varMetadata,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
varMetadata,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
varMetadata<-,AnnotatedDataFrame,data.frame-method | Class Containing Measured Variables and Their Meta-Data Description.
varMetadata<-,eSet,data.frame-method | Class to Contain High-Throughput Assays and Experimental Metadata
Versioned | Class "Versioned"
Versioned-class | Class "Versioned"
VersionedBiobase | Class "VersionedBiobase"
VersionedBiobase-class | Class "VersionedBiobase"
Versions | Class "Versions"
Versions-class | Class "Versions"
VersionsNull | Class "VersionsNull"
VersionsNull-class | Class "VersionsNull"

## -- W --

write.exprs | Class to Contain and Describe High-Throughput Expression Level Assays.
write.exprs,ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.

## -- misc --

[,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
[,container-method | A Lockable List Structure with Constraints on Content
[,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
[,Versions-method | Class "Versions"
[<-,Versions-method | Class "Versions"
[[,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
[[,container-method | A Lockable List Structure with Constraints on Content
[[,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
[[<-,AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
[[<-,container-method | A Lockable List Structure with Constraints on Content
[[<-,eSet-method | Class to Contain High-Throughput Assays and Experimental Metadata
[[<-,Versions-method | Class "Versions"