Biobase: Base functions for Bioconductor

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Documentation for package ‘Biobase’ version 2.48.0

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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.
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