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Biobase (version 2.26.0)

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

2.26.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Biobase (2.26.0)

Aggregate

A Simple Aggregation Mechanism.
anyMissing

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

Retrieve assay data from eSets and ExpressionSets.
Biobase-package

Biobase Package Overview
cache

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

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

Class for Storing Microarray Experiment Information
getPkgVigs

List Vignette Files for a Package
Internals

Internals
annotatedDataFrameFrom-methods

Methods for Function annotatedDataFrameFrom in Package `Biobase'
aggregator

A Simple Class for Aggregators
Versions

Class "Versions"
AnnotatedDataFrame

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

Class "VersionsNull"
dims

Retrieve dimensions of all elements in a list or environment
dumpPackTxt

Dump Textual Description of a Package
featureData

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

Retrieve feature and sample names from eSets.
note

Informational Messages
notes

Retrieve and set eSet notes.
reverseSplit

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

A Lockable List Structure with Constraints on Content
eSet

Class to Contain High-Throughput Assays and Experimental Metadata
NChannelSet-class

Class to contain data from multiple channel array technologies
SnpSet

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

Retrieve and set channel names from object
channel

Create a new ExpressionSet instance by selecting a specific channel
createPackage

Create a Package Directory from a Template
openPDF

Open PDF Files in a Standard Viewer
data:aaMap

Dataset: Names and Characteristics of Amino Acids
read.MIAME

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

Open a Vignette or Show Vignette Selection Menu
readExpressionSet

Read 'ExpressionSet'
strbreak

Break Character Strings to Fit Width
subListExtract

Extract the same element from the sublists of a list
rowMedians

Calculates the median for each row in a matrix
validMsg

Conditionally append result to validity message
classVersion

Retrieve information about versioned classes
MIAxE

MIAxE objects
copyEnv

List-Environment interactions
MultiSet

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

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

Example data.frame representing reporter information
data:geneData

Sample expression matrix and phenotype data.frames.
contents

Function to retrieve contents of environments
data:sample.ExpressionSet

Dataset of class 'ExpressionSet'
data:sample.MultiSet

Data set of class 'MultiSet'
isVersioned

Determine whether object or class contains versioning information
lcSuffix

Compute the longest common prefix or suffix of a string
matchpt

Nearest neighbor search.
multiassign

Assign Values to a Names
protocolData

Protocol Metadata
testBioCConnection

A function to check internet connectivity to Bioconductor
read.AnnotatedDataFrame

Read 'AnnotatedDataFrame'
updateObjectTo

Update an object to the class definition of a template
esApply

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

Retrieve expression data from eSets.
listLen

Lengths of list elements
makeDataPackage

Make an R package from a data object
selectChannels

Create a new NChannelSet instance by selecting specific channels
selectSome

Extract elements of a vector for concise rendering
updateOldESet

Update previously created eSet object to current eSet structure
userQuery

A function to query the user for input
abstract

Retrieve Meta-data from eSets and ExpressionSets.
addVigs2WinMenu

Add Menu Items to an Existing/New Menu of Window
AssayData-class

Class "AssayData"
Versioned

Class "Versioned"
class:characterORMIAME

Class to Make Older Versions Compatible
VersionedBiobase

Class "VersionedBiobase"
Deprecated and Defunct

Biobase Deprecated and Defunct
description

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

Use version information to test whether class is current
isUnique

Determine Unique Elements
package.version

Report Version of a Package
phenoData

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