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Biobase (version 2.30.0)

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

2.30.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Biobase (2.30.0)

Biobase-package

Biobase Package Overview
data:sample.MultiSet

Data set of class 'MultiSet'
selectChannels

Create a new NChannelSet instance by selecting specific channels
exprs

Retrieve expression data from eSets.
esApply

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

Extract elements of a vector for concise rendering
validMsg

Conditionally append result to validity message
Versions

Class "Versions"
MIAxE

MIAxE objects
VersionsNull

Class "VersionsNull"
cache

Evaluate an expression if its value is not already cached.
data:sample.ExpressionSet

Dataset of class 'ExpressionSet'
MultiSet

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

Retrieve and set channel names from object
channel

Create a new ExpressionSet instance by selecting a specific channel
aggregator

A Simple Class for Aggregators
annotatedDataFrameFrom-methods

Methods for Function annotatedDataFrameFrom in Package `Biobase'
Aggregate

A Simple Aggregation Mechanism.
ExpressionSet

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

Class for Storing Microarray Experiment Information
SnpSet

Class to Contain Objects Describing High-Throughput SNP Assays.
Deprecated and Defunct

Biobase Deprecated and Defunct
NChannelSet-class

Class to contain data from multiple channel array technologies
description

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

List Vignette Files for a Package
Internals

Internals
listLen

Lengths of list elements
protocolData

Protocol Metadata
read.AnnotatedDataFrame

Read and write 'AnnotatedDataFrame'
makeDataPackage

Make an R package from a data object
AnnotatedDataFrame

Class Containing Measured Variables and Their Meta-Data Description.
data:geneData

Sample expression matrix and phenotype data.frames.
featureData

Retrieve information on features recorded in eSet-derived classes.
reporter

Example data.frame representing reporter information
featureNames

Retrieve feature and sample names from eSets.
note

Informational Messages
notes

Retrieve and set eSet notes.
ScalarObject-class

Utility classes for length one (scalar) objects
rowQ

A function to compute empirical row quantiles.
snpCall

Get and retrieve SNP call and call probability data.
storageMode

Retrieve or set storage mode for eSets.
abstract

Retrieve Meta-data from eSets and ExpressionSets.
addVigs2WinMenu

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

A Lockable List Structure with Constraints on Content
AssayData-class

Class "AssayData"
class:characterORMIAME

Class to Make Older Versions Compatible
copyEnv

List-Environment interactions
copySubstitute

Copy Between Connections or Files with Configure-Like Name-Value Substitution
isUnique

Determine Unique Elements
isCurrent

Use version information to test whether class is current
openPDF

Open PDF Files in a Standard Viewer
openVignette

Open a Vignette or Show Vignette Selection Menu
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
Versioned

Class "Versioned"
eSet

Class to Contain High-Throughput Assays and Experimental Metadata
createPackage

Create a Package Directory from a Template
VersionedBiobase

Class "VersionedBiobase"
data:aaMap

Dataset: Names and Characteristics of Amino Acids
isVersioned

Determine whether object or class contains versioning information
lcSuffix

Compute the longest common prefix or suffix of a string
package.version

Report Version of a Package
phenoData

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

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

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

Retrieve assay data from eSets and ExpressionSets.
classVersion

Retrieve information about versioned classes
contents

Function to retrieve contents of environments
dims

Retrieve dimensions of all elements in a list or environment
dumpPackTxt

Dump Textual Description of a Package
multiassign

Assign Values to a Names
matchpt

Nearest neighbor search.
testBioCConnection

A function to check internet connectivity to Bioconductor
updateObjectTo

Update an object to the class definition of a template