Biobase: Base functions for Bioconductor


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Documentation for package `Biobase' version 1.10.1

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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

-- --

$,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