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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
2.30.0
2.28.0
2.26.0
Version
2.32.0
License
Artistic-2.0
Maintainer
Bioconductor Package Maintainer
Last Published
February 15th, 2017
Functions in Biobase (2.32.0)
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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