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Biobase (version 2.32.0)

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

2.32.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in Biobase (2.32.0)

ScalarObject-class

Utility classes for length one (scalar) objects
abstract

Retrieve Meta-data from eSets and ExpressionSets.
ExpressionSet

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

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

Example data.frame representing reporter information
AssayData-class

Class "AssayData"
assayData

Retrieve assay data from eSets and ExpressionSets.
rowMedians

Calculates the median for each row in a matrix
description

Retrieve and set overall experimental information eSet-like classes.
class:characterORMIAME

Class to Make Older Versions Compatible
Aggregate

A Simple Aggregation Mechanism.
MIAME

Class for Storing Microarray Experiment Information
cache

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

Class "VersionsNull"
getPkgVigs

List Vignette Files for a Package
createPackage

Create a Package Directory from a Template
AnnotatedDataFrame

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

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

Internals
makeDataPackage

Make an R package from a data object
notes

Retrieve and set eSet notes.
annotatedDataFrameFrom-methods

Methods for Function annotatedDataFrameFrom in Package `Biobase'
featureNames

Retrieve feature and sample names from eSets.
subListExtract

Extract the same element from the sublists of a list
reverseSplit

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

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

Open a Vignette or Show Vignette Selection Menu
data:sample.MultiSet

Data set of class 'MultiSet'
updateOldESet

Update previously created eSet object to current eSet structure
note

Informational Messages
isCurrent

Use version information to test whether class is current
MIAxE

MIAxE objects
rowQ

A function to compute empirical row quantiles.
openPDF

Open PDF Files in a Standard Viewer
userQuery

A function to query the user for input
isUnique

Determine Unique Elements
protocolData

Protocol Metadata
dims

Retrieve dimensions of all elements in a list or environment
selectSome

Extract elements of a vector for concise rendering
addVigs2WinMenu

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

A Simple Class for Aggregators
featureData

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

Retrieve and set channel names from object
package.version

Report Version of a Package
eSet

Class to Contain High-Throughput Assays and Experimental Metadata
strbreak

Break Character Strings to Fit Width
data:geneData

Sample expression matrix and phenotype data.frames.
data:sample.ExpressionSet

Dataset of class 'ExpressionSet'
channel

Create a new ExpressionSet instance by selecting a specific channel
container

A Lockable List Structure with Constraints on Content
exprs

Retrieve expression data from eSets.
Versions

Class "Versions"
listLen

Lengths of list elements
contents

Function to retrieve contents of environments
Biobase-package

Biobase Package Overview
copySubstitute

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

Get and retrieve SNP call and call probability data.
updateObjectTo

Update an object to the class definition of a template
validMsg

Conditionally append result to validity message
Deprecated and Defunct

Biobase Deprecated and Defunct
MultiSet

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

Retrieve information about versioned classes
NChannelSet-class

Class to contain data from multiple channel array technologies
VersionedBiobase

Class "VersionedBiobase"
multiassign

Assign Values to a Names
matchpt

Nearest neighbor search.
copyEnv

List-Environment interactions
phenoData

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

Retrieve or set storage mode for eSets.
readExpressionSet

Read 'ExpressionSet'
data:aaMap

Dataset: Names and Characteristics of Amino Acids
Versioned

Class "Versioned"
esApply

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

Dump Textual Description of a Package
isVersioned

Determine whether object or class contains versioning information
read.AnnotatedDataFrame

Read and write 'AnnotatedDataFrame'
lcSuffix

Compute the longest common prefix or suffix of a string
selectChannels

Create a new NChannelSet instance by selecting specific channels
testBioCConnection

A function to check internet connectivity to Bioconductor