# Biobase: Base functions for Bioconductor

## Documentation for package `Biobase' version 1.8.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E G L M N O P R S T U V W

## -- --

Biobase-package | Biobase Package Overview

## -- A --

aaMap | Dataset: Names and Characteristics of Amino Acids
addVigs2WinMenu | Add Menu Items to an Existing/New Menu of Window
Aggregate | A Simple Aggregation Mechanism.
aggregator | A Simple Class for Aggregators
annotatedDataset | Virtual Superset for 'exprSet', 'eSet' etc.
as.data.frame.exprSet | Class for Microarray Data and Methods for Processing Them
assayData | General Container for High-Throughput Assays and Experimental Metadata

## -- B --

Biobase | Biobase Package Overview

## -- C --

class:aggregator | A Simple Class for Aggregators
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 | General Container for High-Throughput Assays and Experimental Metadata
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:phenoData | Class For Patient or Experiment Level Data
combine | Combine Data Into a Single Object.
container | 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:eset | Dataset of class 'exprSet'
data:exSet | Dataset of class 'exprSet'
data:geneData | A subset of some expression data.
dumpPackTxt | Dump Textual Description of a Package

## -- E --

eList | General Container for High-Throughput Assays and Experimental Metadata
esApply | Apply for the Expression Data in 'exprSet'
eSet | General Container for High-Throughput Assays and Experimental Metadata
eset | Dataset of class 'exprSet'
exprs2excel | Class for Microarray Data and Methods for Processing Them
exprSet | Class for Microarray Data and Methods for Processing Them
exSet | Dataset of class 'exprSet'

## -- G --

geneCovariate | A subset of some expression data.
geneData | A subset of some expression data.
getPkgVigs | List Vignette Files for a Package
golubMergeSub | General Container for High-Throughput Assays and Experimental Metadata

## -- L --

l2e | List-Environment interactions
listLen | List-Environment interactions
listOrEnv | General Container for High-Throughput Assays and Experimental Metadata

## -- M --

MIAME | Class for Storing Microarray Experiment Information
multiassign | Assign Values to a Names

## -- N --

note | Informational Messages

## -- O --

openPDF | Open PDF Files in a Standard Viewer
openVignette | Open a Vignette or Show Vignette Selection Menu

## -- P --

package.version | Report Version of a Package
pData | Class For Patient or Experiment Level Data
phenoData | Class For Patient or Experiment Level Data

## -- 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
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 --

seD | A subset of some expression data.
split | Class for Microarray Data and Methods for Processing Them
strbreak | Break Character Strings to Fit Width
SW | General Container for High-Throughput Assays and Experimental Metadata
SWPD | General Container for High-Throughput Assays and Experimental Metadata
swrep | General Container for 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

## -- V --

varMetadata | Class For Patient or Experiment Level Data

## -- W --

write.exprs | Class for Microarray Data and Methods for Processing Them