Biobase: Base functions for Bioconductor

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Documentation for package ‘Biobase’ version 2.12.2

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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.
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 Methods for Function combine in Package 'Biobase'
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
combine-method Methods for Function combine in Package 'Biobase'
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.
dims Retrieve dimensions of all elements in a list or environment
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.
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.
getObjectSlots Update an object to its current class definition
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
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 Update an object to its current class definition
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
updateObject-method Update an object to its current class definition
updateObjectFromSlots Update an object to its current class definition
updateObjectTo Update an object to its current class definition
updateObjectTo-method Class to Contain High-Throughput Assays and Experimental Metadata
updateObjectTo-method Update an object to its current class definition
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