# Biobase: Base functions for Bioconductor

## Documentation for package ‘Biobase’ version 2.16.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## 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

## -- A --

aaMap | Dataset: Names and Characteristics of Amino Acids
abstract | Retrieve Meta-data from eSets and ExpressionSets.
abstract-method | Class for Storing Microarray Experiment Information
abstract-method | Class to Contain High-Throughput Assays and Experimental Metadata
addVigs2WinMenu | Add Menu Items to an Existing/New Menu of Window
aggenv-method | A Simple Class for Aggregators
aggfun-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.
AnnotatedDataFrame-method | Class Containing Measured Variables and Their Meta-Data Description.
annotatedDataFrameFrom | Methods for Function annotatedDataFrameFrom in Package 'Biobase'
annotatedDataFrameFrom-method | Methods for Function annotatedDataFrameFrom in Package 'Biobase'
annotation | Annotate eSet data.
annotation-method | Class to Contain High-Throughput Assays and Experimental Metadata
annotation<- | Annotate eSet data.
annotation<--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-class | Class "AssayData"
assayData-method | Class "AssayData"
assayData-method | Class to Contain High-Throughput Assays and Experimental Metadata
assayData<- | Retrieve assay data from eSets and ExpressionSets.
assayData<--method | Class to Contain High-Throughput Assays and Experimental Metadata
assayDataElement | 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-method | Class to contain data from multiple channel array technologies
channelNames | Retrieve channel names from object
channelNames-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:MIAxE | MIAxE objects
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-method | Class "Versioned"
classVersion-method | Retrieve information about versioned classes
classVersion<- | Retrieve information about versioned classes
classVersion<--method | Class "Versioned"
coerce-method | Class Containing Measured Variables and Their Meta-Data Description.
coerce-method | Class to Contain and Describe High-Throughput Expression Level Assays.
coerce-method | Class to Contain and Describe High-Throughput Expression Level Assays.
coerce-method | Class "Versions"
combine-method | Class Containing Measured Variables and Their Meta-Data Description.
combine-method | Class "AssayData"
combine-method | Class for Storing Microarray Experiment Information
combine-method | Class to Contain High-Throughput Assays and Experimental Metadata
Compare-method | Class "Versions"
conditions | Accessors and generic functions used in the context of count datasets
conditions<- | Accessors and generic functions used in the context of count datasets
container | A Lockable List Structure with Constraints on Content
container-class | A Lockable List Structure with Constraints on Content
content-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
counts | Accessors and generic functions used in the context of count datasets
counts<- | Accessors and generic functions used in the context of count datasets
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-method | Class to Contain High-Throughput Assays and Experimental Metadata
description<- | Retrieve and set overall experimental information eSet-like classes.
description<--method | Class to Contain High-Throughput Assays and Experimental Metadata
design | Accessors and generic functions used in the context of count datasets
design<- | Accessors and generic functions used in the context of count datasets
dim-method | Class Containing Measured Variables and Their Meta-Data Description.
dim-method | Class to Contain High-Throughput Assays and Experimental Metadata
dimLabels | Class Containing Measured Variables and Their Meta-Data Description.
dimLabels-method | Class Containing Measured Variables and Their Meta-Data Description.
dimLabels<- | Class Containing Measured Variables and Their Meta-Data Description.
dimLabels<--method | Class Containing Measured Variables and Their Meta-Data Description.
dims | Retrieve dimensions of all elements in a list or environment
dims-method | Class to Contain High-Throughput Assays and Experimental Metadata
dispTable | Accessors and generic functions used in the context of count datasets
dispTable<- | Accessors and generic functions used in the context of count datasets
dumpPackTxt | Dump Textual Description of a Package

## -- E --

esApply | An apply-like function for ExpressionSet and related structures.
esApply-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
estimateDispersions | Accessors and generic functions used in the context of count datasets
estimateSizeFactors | Accessors and generic functions used in the context of count datasets
experimentData | Retrieve Meta-data from eSets and ExpressionSets.
experimentData-method | Class to Contain High-Throughput Assays and Experimental Metadata
experimentData<- | Retrieve Meta-data from eSets and ExpressionSets.
experimentData<--method | Class to Contain High-Throughput Assays and Experimental Metadata
expinfo-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.
ExpressionSet-method | Class to Contain and Describe High-Throughput Expression Level Assays.
exprs | Retrieve expression data from eSets.
exprs-method | Class to Contain and Describe High-Throughput Expression Level Assays.
exprs-method | Class to Contain Objects Describing High-Throughput SNP Assays.
exprs-method | Class to Contain High-Throughput Assays and Experimental Metadata
exprs<- | Retrieve expression data from eSets.
exprs<--method | Class to Contain and Describe High-Throughput Expression Level Assays.
exprs<--method | Class to Contain Objects Describing High-Throughput SNP Assays.
exprs<--method | Class to Contain High-Throughput Assays and Experimental Metadata

## -- F --

fData | Retrieve information on features recorded in eSet-derived classes.
fData-method | Class to Contain High-Throughput Assays and Experimental Metadata
fData<- | Retrieve information on features recorded in eSet-derived classes.
fData<--method | Class to Contain High-Throughput Assays and Experimental Metadata
featureData | Retrieve information on features recorded in eSet-derived classes.
featureData-method | Class to Contain High-Throughput Assays and Experimental Metadata
featureData<- | Retrieve information on features recorded in eSet-derived classes.
featureData<--method | Class to Contain High-Throughput Assays and Experimental Metadata
featureNames | Retrieve feature and sample names from eSets.
featureNames-method | Class Containing Measured Variables and Their Meta-Data Description.
featureNames-method | Class "AssayData"
featureNames-method | Class to Contain High-Throughput Assays and Experimental Metadata
featureNames<- | Retrieve feature and sample names from eSets.
featureNames<--method | Class Containing Measured Variables and Their Meta-Data Description.
featureNames<--method | Class "AssayData"
featureNames<--method | Class to Contain High-Throughput Assays and Experimental Metadata
fvarLabels | Retrieve information on features recorded in eSet-derived classes.
fvarLabels-method | Class to Contain High-Throughput Assays and Experimental Metadata
fvarLabels<- | Retrieve information on features recorded in eSet-derived classes.
fvarLabels<--method | Class to Contain High-Throughput Assays and Experimental Metadata
fvarMetadata | Retrieve information on features recorded in eSet-derived classes.
fvarMetadata-method | Class to Contain High-Throughput Assays and Experimental Metadata
fvarMetadata<- | Retrieve information on features recorded in eSet-derived classes.
fvarMetadata<--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.
getPkgVigs | List Vignette Files for a Package

## -- H --

hybridizations-method | Class for Storing Microarray Experiment Information

## -- I --

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

## -- L --

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-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-method | A Lockable List Structure with Constraints on Content

## -- M --

makeDataPackage | Make an R package from a data object
makeDataPackage-method | Class to Contain and Describe High-Throughput Expression Level Assays.
makeDataPackage-method | Make an R package from a data object
matchpt | Nearest neighbor search.
MIAME | Class for Storing Microarray Experiment Information
MIAME-class | Class for Storing Microarray Experiment Information
MIAxE | MIAxE objects
MIAxE-class | MIAxE objects
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-method | Class Containing Measured Variables and Their Meta-Data Description.
ncol-method | Class to Contain High-Throughput Assays and Experimental Metadata
normControls-method | Class for Storing Microarray Experiment Information
note | Informational Messages
notes | Retrieve and set eSet notes.
notes-method | Class for Storing Microarray Experiment Information
notes-method | Class to Contain High-Throughput Assays and Experimental Metadata
notes<- | Retrieve and set eSet notes.
notes<--method | Class for Storing Microarray Experiment Information
notes<--method | Class to Contain High-Throughput Assays and Experimental Metadata

## -- O --

openPDF | Open PDF Files in a Standard Viewer
openVignette | Open a Vignette or Show Vignette Selection Menu
otherInfo-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-method | Class Containing Measured Variables and Their Meta-Data Description.
pData-method | Class to Contain High-Throughput Assays and Experimental Metadata
pData<- | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
pData<--method | Class Containing Measured Variables and Their Meta-Data Description.
pData<--method | Class to Contain High-Throughput Assays and Experimental Metadata
phenoData | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
phenoData-method | Class to Contain High-Throughput Assays and Experimental Metadata
phenoData<- | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
phenoData<--method | Class to Contain High-Throughput Assays and Experimental Metadata
preproc | Class for Storing Microarray Experiment Information
preproc-method | Class for Storing Microarray Experiment Information
preproc-method | Class to Contain High-Throughput Assays and Experimental Metadata
preproc<- | Class for Storing Microarray Experiment Information
preproc<--method | Class for Storing Microarray Experiment Information
preproc<--method | Class to Contain High-Throughput Assays and Experimental Metadata
protocolData | Protocol Metadata
protocolData-method | Class to Contain High-Throughput Assays and Experimental Metadata
protocolData<- | Protocol Metadata
protocolData<--method | Class to Contain High-Throughput Assays and Experimental Metadata
protocolData<--method | Protocol Metadata
pubMedIds | Retrieve Meta-data from eSets and ExpressionSets.
pubMedIds-method | Class for Storing Microarray Experiment Information
pubMedIds-method | Class to Contain High-Throughput Assays and Experimental Metadata
pubMedIds<- | Retrieve Meta-data from eSets and ExpressionSets.
pubMedIds<--method | Class for Storing Microarray Experiment Information
pubMedIds<--method | Class to Contain High-Throughput Assays and Experimental Metadata

## -- 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-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-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-method | Class Containing Measured Variables and Their Meta-Data Description.
sampleNames-method | Class "AssayData"
sampleNames-method | Class to contain data from multiple channel array technologies
sampleNames-method | Class to Contain High-Throughput Assays and Experimental Metadata
sampleNames<- | Retrieve feature and sample names from eSets.
sampleNames<--method | Class Containing Measured Variables and Their Meta-Data Description.
sampleNames<--method | Class "AssayData"
sampleNames<--method | Class to contain data from multiple channel array technologies
sampleNames<--method | Class to Contain High-Throughput Assays and Experimental Metadata
samples | Class for Storing Microarray Experiment Information
samples-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
ScalarLogical-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-method | Class to contain data from multiple channel array technologies
selectSome | Extract elements of a vector for concise rendering
show-method | Utility classes for length one (scalar) objects
show-method | Class Containing Measured Variables and Their Meta-Data Description.
show-method | Class for Storing Microarray Experiment Information
show-method | MIAxE objects
show-method | Class "Versioned"
show-method | Class "Versions"
show-method | Class "VersionsNull"
show-method | A Lockable List Structure with Constraints on Content
show-method | Class to Contain High-Throughput Assays and Experimental Metadata
sizeFactors | Accessors and generic functions used in the context of count datasets
sizeFactors<- | Accessors and generic functions used in the context of count datasets
snpCall | Get and retrieve SNP call and call probability data.
snpCall-method | Class to Contain Objects Describing High-Throughput SNP Assays.
snpCall<- | Get and retrieve SNP call and call probability data.
snpCall<--method | Class to Contain Objects Describing High-Throughput SNP Assays.
snpCallProbability | Get and retrieve SNP call and call probability data.
snpCallProbability-method | Class to Contain Objects Describing High-Throughput SNP Assays.
snpCallProbability<- | Get and retrieve SNP call and call probability data.
snpCallProbability<--method | Class to Contain Objects Describing High-Throughput SNP Assays.
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-method | Class "AssayData"
storageMode-method | Class to Contain High-Throughput Assays and Experimental Metadata
storageMode<- | Retrieve or set storage mode for eSets.
storageMode<--method | Class "AssayData"
storageMode<--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-method | Class Containing Measured Variables and Their Meta-Data Description.
updateObject-method | Class to Contain and Describe High-Throughput Expression Level Assays.
updateObject-method | Class for Storing Microarray Experiment Information
updateObject-method | Class "Versions"
updateObject-method | Class to Contain High-Throughput Assays and Experimental Metadata
updateObjectTo | Update an object to the class definition of a template
updateObjectTo-method | Class to Contain High-Throughput Assays and Experimental Metadata
updateObjectTo-method | Update an object to the class definition of a template
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-method | Class Containing Measured Variables and Their Meta-Data Description.
varLabels-method | Class to Contain High-Throughput Assays and Experimental Metadata
varLabels<- | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
varLabels<--method | Class Containing Measured Variables and Their Meta-Data Description.
varLabels<--method | Class to Contain High-Throughput Assays and Experimental Metadata
varMetadata | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
varMetadata-method | Class Containing Measured Variables and Their Meta-Data Description.
varMetadata-method | Class to Contain High-Throughput Assays and Experimental Metadata
varMetadata<- | Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
varMetadata<--method | Class Containing Measured Variables and Their Meta-Data Description.
varMetadata<--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-method | Class to Contain and Describe High-Throughput Expression Level Assays.

## -- misc --

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