Biobase: Base functions for Bioconductor

Documentation for package `Biobase' version 1.10.1

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-- --

Biobase-package

Biobase Package Overview

-- --

$,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
$,annotatedDataset-method	Virtual Superset for 'exprSet', 'eSet' etc.
$,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
$,phenoData-method	Class For Patient or Experiment Level Data
$<-,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
$<-,annotatedDataset-method	Virtual Superset for 'exprSet', 'eSet' etc.
$<-,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
$<-,phenoData-method	Class For Patient or Experiment Level Data

-- A --

aaMap	Dataset: Names and Characteristics of Amino Acids
abstract	Retrieve feature and sample names from eSets and exprSets.
abstract,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
abstract,exprSet-method	Class for Microarray Data and Methods for Processing Them
abstract,MIAME-method	Class for Storing Microarray Experiment Information
addVigs2WinMenu	Add Menu Items to an Existing/New Menu of Window
aggenv,aggregator-method	A Simple Class for Aggregators
aggfun,aggregator-method	A Simple Class for Aggregators
Aggregate	A Simple Aggregation Mechanism.
aggregator	A Simple Class for Aggregators
aggregator-class	A Simple Class for Aggregators
AnnotatedDataFrame	Class to Contain Measured Variables and Their Meta-Data Description.
AnnotatedDataFrame-class	Class to Contain Measured Variables and Their Meta-Data Description.
annotatedDataset	Virtual Superset for 'exprSet', 'eSet' etc.
annotatedDataset-class	Virtual Superset for 'exprSet', 'eSet' etc.
annotation	Annotate eSet data.
annotation,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
annotation,exprSet-method	Class for Microarray Data and Methods for Processing Them
annotation<-,eSet,character-method	Class to Contain High-Throughput Assays and Experimental Metadata
annotation<-,exprSet-method	Class for Microarray Data and Methods for Processing Them
as.data.frame.exprSet	Class for Microarray Data and Methods for Processing Them
as.data.frame.exprSet,exprSet-method	Class for Microarray Data and Methods for Processing Them
AssayData	Class "AssayData"
assayData	Retrieve assay data from eSets and exprSets.
assayData,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
assayData,exprSet-method	Class for Microarray Data and Methods for Processing Them
AssayData-class	Class "AssayData"
assayData<-,eSet,AssayData-method	Class to Contain High-Throughput Assays and Experimental Metadata
assayDataElement	Class "AssayData"
assayDataElementNames	Class "AssayData"
assayDataElementReplace	Class "AssayData"
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.
characterORMIAME-class	Class to Make Older Versions Compatible
class:aggregator	A Simple Class for Aggregators
class:AnnotatedDataFrame	Class to Contain Measured Variables and Their Meta-Data Description.
class:annotatedDataset	Virtual Superset for 'exprSet', 'eSet' etc.
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:exprList	Class Union of a List and an Environment
class:exprMatrix	Class Union for Objects Behaving Like a Matrix
class:exprSet	Class for Microarray Data and Methods for Processing Them
class:MIAME	Class for Storing Microarray Experiment Information
class:MultiSet	Class to Contain and Describe High-Throughput Expression Level Assays.
class:phenoData	Class For Patient or Experiment Level Data
class:SnpSet	Class to Contain Objects Describing High-Throughput SNP Assays.
coerce,data.frame,phenoData-method	Class For Patient or Experiment Level Data
coerce,exprSet,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
coerce,exprSet,ExpressionSet-method	Class to Contain and Describe High-Throughput Expression Level Assays.
coerce,phenoData,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
combine	Combine Data Into a Single Object.
combine,AnnotatedDataFrame,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
combine,AssayData,AssayData-method	Class "AssayData"
combine,eSet,ANY-method	Class to Contain High-Throughput Assays and Experimental Metadata
combine,eSet,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
combine,MIAME,MIAME-method	Class for Storing Microarray Experiment Information
combine,phenoData,ANY-method	Class For Patient or Experiment Level Data
combine,phenoData,phenoData-method	Class For Patient or Experiment Level Data
container	A Lockable List Structure with Constraints on Content
container-class	A Lockable List Structure with Constraints on Content
content,container-method	A Lockable List Structure with Constraints on Content
contents	Function to retrieve contents of environments
convertVarLabels,phenoData-method	Class For Patient or Experiment Level Data
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:eset	(Deprecated) dataset of class 'exprSet'
data:geneData	A subset of some expression data.
data:sample.eSet	Dataset of class 'eSet'
data:sample.ExpressionSet	Dataset of class 'ExpressionSet'
data:sample.exprSet	Dataset of class 'exprSet'
data:sample.exprSet.1	Dataset of class 'exprSet'
description	Retrieve and set overall experimental information eSet-like classes.
description,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
description,exprSet-method	Class for Microarray Data and Methods for Processing Them
description<-,eSet,MIAME-method	Class to Contain High-Throughput Assays and Experimental Metadata
description<-,exprSet-method	Class for Microarray Data and Methods for Processing Them
dim,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
dim,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
dims	Retrieve dimensions of all elements in a list or environment
dims,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
dumpPackTxt	Dump Textual Description of a Package

-- E --

esApply	Apply for the Expression Data in 'exprSet'
eSet	Class to Contain High-Throughput Assays and Experimental Metadata
eset	(Deprecated) dataset of class 'exprSet'
eSet-class	Class to Contain High-Throughput Assays and Experimental Metadata
experimentData	Retrieve feature and sample names from eSets and exprSets.
experimentData,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
experimentData<-,eSet,MIAME-method	Class to Contain High-Throughput Assays and Experimental Metadata
expinfo,MIAME-method	Class for Storing Microarray Experiment Information
ExpressionSet	Class to Contain and Describe High-Throughput Expression Level Assays.
ExpressionSet-class	Class to Contain and Describe High-Throughput Expression Level Assays.
exprMatrix-class	Class Union for Objects Behaving Like a Matrix
exprs	Retrieve expression data from eSets.
exprs,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
exprs,ExpressionSet-method	Class to Contain and Describe High-Throughput Expression Level Assays.
exprs,exprSet-method	Class for Microarray Data and Methods for Processing Them
exprs,SnpSet-method	Class to Contain Objects Describing High-Throughput SNP Assays.
exprs2excel	Class for Microarray Data and Methods for Processing Them
exprs2excel,exprSet-method	Class for Microarray Data and Methods for Processing Them
exprs<-,eSet,AssayData-method	Class to Contain High-Throughput Assays and Experimental Metadata
exprs<-,ExpressionSet,matrix-method	Class to Contain and Describe High-Throughput Expression Level Assays.
exprs<-,exprSet-method	Class for Microarray Data and Methods for Processing Them
exprs<-,SnpSet,matrix-method	Class to Contain Objects Describing High-Throughput SNP Assays.
exprSet	Class for Microarray Data and Methods for Processing Them
exprSet-class	Class for Microarray Data and Methods for Processing Them

-- F --

featureNames	Retrieve feature and sample names from eSets and exprSets.
featureNames,AssayData-method	Class "AssayData"
featureNames,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
featureNames<-,AssayData-method	Class "AssayData"
featureNames<-,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata

-- G --

geneCovariate	A subset of some expression data.
geneData	A subset of some expression data.
geneNames	Retrieve feature and sample names from eSets and exprSets.
geneNames,exprSet-method	Class for Microarray Data and Methods for Processing Them
geneNames<-,exprSet-method	Class for Microarray Data and Methods for Processing Them
getExpData,eSet,character-method	Class to Contain High-Throughput Assays and Experimental Metadata
getPkgVigs	List Vignette Files for a Package
getVarMetadata	Class For Patient or Experiment Level Data
getVarMetadata,phenoData,character,character-method	Class For Patient or Experiment Level Data
getVarMetadata,phenoData,character,missing-method	Class For Patient or Experiment Level Data
golubMergeSub	Class to Contain High-Throughput Assays and Experimental Metadata

-- H --

hybridizations,MIAME-method

Class for Storing Microarray Experiment Information

-- I --

initfun,aggregator-method	A Simple Class for Aggregators
initialize,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
initialize,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
initialize,ExpressionSet-method	Class to Contain and Describe High-Throughput Expression Level Assays.
initialize,MultiSet-method	Class to Contain and Describe High-Throughput Expression Level Assays.
initialize,SnpSet-method	Class to Contain Objects Describing High-Throughput SNP Assays.
isUnique	Determine Unique Elements
iter,exprSet,character,function-method	Class for Microarray Data and Methods for Processing Them
iter,exprSet,missing,function-method	Class for Microarray Data and Methods for Processing Them
iter,exprSet,missing,list-method	Class for Microarray Data and Methods for Processing Them

-- L --

l2e	List-Environment interactions
length,container-method	A Lockable List Structure with Constraints on Content
listLen	List-Environment interactions
listOrEnv	Class to Contain High-Throughput Assays and Experimental Metadata
locked,container-method	A Lockable List Structure with Constraints on Content

-- M --

matchpt	Finds Nearest Neighbours for Sets of Points given by NxD Coordinates
MIAME	Class for Storing Microarray Experiment Information
MIAME-class	Class for Storing Microarray Experiment Information
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 --

ncol,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
ncol,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
normControls,MIAME-method	Class for Storing Microarray Experiment Information
note	Informational Messages
notes	Retrieve and set eSet and exprSet notes.
notes,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
notes,exprSet-method	Class for Microarray Data and Methods for Processing Them
notes,MIAME-method	Class for Storing Microarray Experiment Information
notes<-,eSet,list-method	Class to Contain High-Throughput Assays and Experimental Metadata
notes<-,exprSet-method	Class for Microarray Data and Methods for Processing Them
notes<-,MIAME,list-method	Class for Storing Microarray Experiment Information

-- O --

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

-- P --

package.version	Report Version of a Package
pData	Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
pData,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
pData,annotatedDataset-method	Virtual Superset for 'exprSet', 'eSet' etc.
pData,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
pData,phenoData-method	Class For Patient or Experiment Level Data
pData<-,AnnotatedDataFrame,data.frame-method	Class to Contain Measured Variables and Their Meta-Data Description.
pData<-,annotatedDataset,ANY-method	Virtual Superset for 'exprSet', 'eSet' etc.
pData<-,eSet,data.frame-method	Class to Contain High-Throughput Assays and Experimental Metadata
pData<-,phenoData,ANY-method	Class For Patient or Experiment Level Data
phenoData	Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
phenoData,annotatedDataset-method	Virtual Superset for 'exprSet', 'eSet' etc.
phenoData,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
phenoData-class	Class For Patient or Experiment Level Data
phenoData<-,annotatedDataset,phenoData-method	Class For Patient or Experiment Level Data
phenoData<-,eSet,AnnotatedDataFrame-method	Class to Contain High-Throughput Assays and Experimental Metadata
preproc,MIAME-method	Class for Storing Microarray Experiment Information
pubMedIds	Retrieve feature and sample names from eSets and exprSets.
pubMedIds,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
pubMedIds,MIAME-method	Class for Storing Microarray Experiment Information
pubMedIds<-,eSet,character-method	Class to Contain High-Throughput Assays and Experimental Metadata
pubMedIds<-,MIAME,ANY-method	Class for Storing Microarray Experiment Information

-- R --

read.exprSet	Read Experimental Data and into an 'exprSet' Object
read.MIAME	Read MIAME Information into an Instance of Class 'MIAME'
read.phenoData	Read 'phenoData'
reporter	Example Data Frame Object for the ReporterInfo Slot
reporterInfo	Retrieve and set information about reporters.
reporterInfo,annotatedDataset-method	Virtual Superset for 'exprSet', 'eSet' etc.
reporterInfo<-,annotatedDataset,data.frame-method	Virtual Superset for 'exprSet', 'eSet' etc.
reporterNames,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
reverseSplit	A function to reverse the role of names and values in a list.
rowMax	A function to compute empirical row quantiles.
rowMedians	A function to compute empirical row quantiles.
rowMin	A function to compute empirical row quantiles.
rowQ	A function to compute empirical row quantiles.

-- S --

sample.eSet	Dataset of class 'eSet'
sample.ExpressionSet	Dataset of class 'ExpressionSet'
sample.exprSet	Dataset of class 'exprSet'
sample.exprSet.1	Dataset of class 'exprSet'
sampleNames	Retrieve feature and sample names from eSets and exprSets.
sampleNames,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
sampleNames,AssayData-method	Class "AssayData"
sampleNames,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
sampleNames,exprSet-method	Class for Microarray Data and Methods for Processing Them
sampleNames<-,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
sampleNames<-,AssayData-method	Class "AssayData"
sampleNames<-,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
sampleNames<-,exprSet-method	Class for Microarray Data and Methods for Processing Them
samples	Class for Storing Microarray Experiment Information
samples,MIAME-method	Class for Storing Microarray Experiment Information
se.exprs	Retrieve expression data from eSets.
se.exprs,exprSet-method	Class for Microarray Data and Methods for Processing Them
se.exprs<-,exprSet-method	Class for Microarray Data and Methods for Processing Them
seD	A subset of some expression data.
show,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
show,container-method	A Lockable List Structure with Constraints on Content
show,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
show,exprSet-method	Class for Microarray Data and Methods for Processing Them
show,MIAME-method	Class for Storing Microarray Experiment Information
show,phenoData-method	Class For Patient or Experiment Level Data
SnpSet	Class to Contain Objects Describing High-Throughput SNP Assays.
SnpSet-class	Class to Contain Objects Describing High-Throughput SNP Assays.
split	Class for Microarray Data and Methods for Processing Them
split,exprSet,factor,missing-method	Class for Microarray Data and Methods for Processing Them
split,exprSet,vector,missing-method	Class for Microarray Data and Methods for Processing Them
split,phenoData,vector,missing-method	Class For Patient or Experiment Level Data
storageMode	Retrieve or set storage mode for eSets.
storageMode,AssayData-method	Class "AssayData"
storageMode,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
storageMode<-,AssayData,character-method	Class "AssayData"
storageMode<-,eSet,character-method	Class to Contain High-Throughput Assays and Experimental Metadata
strbreak	Break Character Strings to Fit Width
SW	Class to Contain High-Throughput Assays and Experimental Metadata
SWPD	Class to Contain High-Throughput Assays and Experimental Metadata
swrep	Class to Contain High-Throughput Assays and Experimental Metadata

-- T --

testBioCConnection

A function to check internet connectivity to Bioconductor

-- U --

update2MIAME	Class for Microarray Data and Methods for Processing Them
update2MIAME,exprSet-method	Class for Microarray Data and Methods for Processing Them
updateOldESet	Update previously created eSet object to current eSet structure

-- V --

varLabels	Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
varLabels,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
varLabels,annotatedDataset-method	Virtual Superset for 'exprSet', 'eSet' etc.
varLabels,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
varLabels,phenoData-method	Class For Patient or Experiment Level Data
varLabels<-,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
varLabels<-,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
varMetadata	Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes.
varMetadata,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
varMetadata,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
varMetadata,phenoData-method	Class For Patient or Experiment Level Data
varMetadata<-,AnnotatedDataFrame,data.frame-method	Class to Contain Measured Variables and Their Meta-Data Description.
varMetadata<-,eSet,data.frame-method	Class to Contain High-Throughput Assays and Experimental Metadata

-- W --

write.exprs	Class for Microarray Data and Methods for Processing Them
write.exprs,exprSet-method	Class for Microarray Data and Methods for Processing Them

-- misc --

[,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
[,container-method	A Lockable List Structure with Constraints on Content
[,eSet-method	Class to Contain High-Throughput Assays and Experimental Metadata
[,exprSet-method	Class for Microarray Data and Methods for Processing Them
[,phenoData-method	Class For Patient or Experiment Level Data
[[,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
[[,annotatedDataset-method	Virtual Superset for 'exprSet', 'eSet' etc.
[[,container-method	A Lockable List Structure with Constraints on Content
[[,phenoData-method	Class For Patient or Experiment Level Data
[[<-,AnnotatedDataFrame-method	Class to Contain Measured Variables and Their Meta-Data Description.
[[<-,annotatedDataset-method	Virtual Superset for 'exprSet', 'eSet' etc.
[[<-,container-method	A Lockable List Structure with Constraints on Content
[[<-,phenoData-method	Class For Patient or Experiment Level Data