Biobase: Base functions for Bioconductor

---

Documentation for package ‘Biobase’ version 2.54.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• 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-method	Class to Contain High-Throughput Assays and Experimental Metadata
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 data from multiple channel array technologies
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

-- 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 and set channel names from object
channelNames-method	Class to contain data from multiple channel array technologies
channelNames<-	Retrieve and set 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"
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
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
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.
dimnames	Class to Contain High-Throughput Assays and Experimental Metadata
dimnames-method	Class Containing Measured Variables and Their Meta-Data Description.
dimnames-method	Class to Contain High-Throughput Assays and Experimental Metadata
dimnames<-	Class to Contain High-Throughput Assays and Experimental Metadata
dimnames<--method	Class Containing Measured Variables and Their Meta-Data Description.
dimnames<--method	Class to Contain High-Throughput Assays and Experimental Metadata
dims	Class to Contain High-Throughput Assays and Experimental Metadata
dims-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-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-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 --

head.AnnotatedDataFrame	Class Containing Measured Variables and Their Meta-Data Description.
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 and write '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
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 --

tail.AnnotatedDataFrame	Class Containing Measured Variables and Their Meta-Data Description.
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.AnnotatedDataFrame	Read and write 'AnnotatedDataFrame'
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