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Biobase (version 2.28.0)

Biobase: Base functions for Bioconductor

Description

Functions that are needed by many other packages or which replace R functions.

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Version

Version

2.28.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Biobase (2.28.0)

AssayData-class

Class "AssayData"
Versions

Class "Versions"
VersionsNull

Class "VersionsNull"
esApply

An apply-like function for ExpressionSet and related structures.
listLen

Lengths of list elements
exprs

Retrieve expression data from eSets.
makeDataPackage

Make an R package from a data object
class:characterORMIAME

Class to Make Older Versions Compatible
abstract

Retrieve Meta-data from eSets and ExpressionSets.
addVigs2WinMenu

Add Menu Items to an Existing/New Menu of Window
ExpressionSet

Class to Contain and Describe High-Throughput Expression Level Assays.
MIAME

Class for Storing Microarray Experiment Information
NChannelSet-class

Class to contain data from multiple channel array technologies
createPackage

Create a Package Directory from a Template
data:aaMap

Dataset: Names and Characteristics of Amino Acids
SnpSet

Class to Contain Objects Describing High-Throughput SNP Assays.
isVersioned

Determine whether object or class contains versioning information
selectSome

Extract elements of a vector for concise rendering
lcSuffix

Compute the longest common prefix or suffix of a string
selectChannels

Create a new NChannelSet instance by selecting specific channels
protocolData

Protocol Metadata
read.AnnotatedDataFrame

Read and write 'AnnotatedDataFrame'
validMsg

Conditionally append result to validity message
assayData

Retrieve assay data from eSets and ExpressionSets.
anyMissing

Checks if there are any missing values in an object or not
container

A Lockable List Structure with Constraints on Content
cache

Evaluate an expression if its value is not already cached.
Biobase-package

Biobase Package Overview
eSet

Class to Contain High-Throughput Assays and Experimental Metadata
MultiSet

Class to Contain and Describe High-Throughput Expression Level Assays.
MIAxE

MIAxE objects
classVersion

Retrieve information about versioned classes
contents

Function to retrieve contents of environments
VersionedBiobase

Class "VersionedBiobase"
Versioned

Class "Versioned"
data:geneData

Sample expression matrix and phenotype data.frames.
reporter

Example data.frame representing reporter information
featureNames

Retrieve feature and sample names from eSets.
featureData

Retrieve information on features recorded in eSet-derived classes.
data:sample.ExpressionSet

Dataset of class 'ExpressionSet'
data:sample.MultiSet

Data set of class 'MultiSet'
openVignette

Open a Vignette or Show Vignette Selection Menu
openPDF

Open PDF Files in a Standard Viewer
read.MIAME

Read MIAME Information into an Instance of Class 'MIAME'
readExpressionSet

Read 'ExpressionSet'
strbreak

Break Character Strings to Fit Width
subListExtract

Extract the same element from the sublists of a list
phenoData

Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
package.version

Report Version of a Package
updateObjectTo

Update an object to the class definition of a template
testBioCConnection

A function to check internet connectivity to Bioconductor
Aggregate

A Simple Aggregation Mechanism.
annotatedDataFrameFrom-methods

Methods for Function annotatedDataFrameFrom in Package `Biobase'
aggregator

A Simple Class for Aggregators
AnnotatedDataFrame

Class Containing Measured Variables and Their Meta-Data Description.
dims

Retrieve dimensions of all elements in a list or environment
dumpPackTxt

Dump Textual Description of a Package
isCurrent

Use version information to test whether class is current
matchpt

Nearest neighbor search.
multiassign

Assign Values to a Names
reverseSplit

A function to reverse the role of names and values in a list.
isUnique

Determine Unique Elements
rowMedians

Calculates the median for each row in a matrix
updateOldESet

Update previously created eSet object to current eSet structure
userQuery

A function to query the user for input
channel

Create a new ExpressionSet instance by selecting a specific channel
channelNames

Retrieve and set channel names from object
copyEnv

List-Environment interactions
copySubstitute

Copy Between Connections or Files with Configure-Like Name-Value Substitution
Deprecated and Defunct

Biobase Deprecated and Defunct
description

Retrieve and set overall experimental information eSet-like classes.
getPkgVigs

List Vignette Files for a Package
Internals

Internals
note

Informational Messages
notes

Retrieve and set eSet notes.
rowQ

A function to compute empirical row quantiles.
ScalarObject-class

Utility classes for length one (scalar) objects
snpCall

Get and retrieve SNP call and call probability data.
storageMode

Retrieve or set storage mode for eSets.