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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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2.32.0
2.30.0
2.28.0
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Version
2.30.0
License
Artistic-2.0
Maintainer
Bioconductor Package Maintainer
Last Published
January 1st, 1970
Functions in Biobase (2.30.0)
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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