Biobase v2.28.0

Biobase: Base functions for Bioconductor

Functions that are needed by many other packages or which replace R functions.

Functions in Biobase

Name Description
AssayData-class Class "AssayData"
Versions Class "Versions"
VersionsNull Class "VersionsNull"
esApply An apply-like function for ExpressionSet and related structures.
listLen Lengths of list elements
exprs Retrieve expression data from eSets.
makeDataPackage Make an R package from a data object
class:characterORMIAME Class to Make Older Versions Compatible
abstract Retrieve Meta-data from eSets and ExpressionSets.
addVigs2WinMenu Add Menu Items to an Existing/New Menu of Window
ExpressionSet Class to Contain and Describe High-Throughput Expression Level Assays.
MIAME Class for Storing Microarray Experiment Information
NChannelSet-class Class to contain data from multiple channel array technologies
createPackage Create a Package Directory from a Template
data:aaMap Dataset: Names and Characteristics of Amino Acids
SnpSet Class to Contain Objects Describing High-Throughput SNP Assays.
isVersioned Determine whether object or class contains versioning information
selectSome Extract elements of a vector for concise rendering
lcSuffix Compute the longest common prefix or suffix of a string
selectChannels Create a new NChannelSet instance by selecting specific channels
protocolData Protocol Metadata
read.AnnotatedDataFrame Read and write 'AnnotatedDataFrame'
validMsg Conditionally append result to validity message
assayData Retrieve assay data from eSets and ExpressionSets.
anyMissing Checks if there are any missing values in an object or not
container A Lockable List Structure with Constraints on Content
cache Evaluate an expression if its value is not already cached.
Biobase-package Biobase Package Overview
eSet Class to Contain High-Throughput Assays and Experimental Metadata
MultiSet Class to Contain and Describe High-Throughput Expression Level Assays.
MIAxE MIAxE objects
classVersion Retrieve information about versioned classes
contents Function to retrieve contents of environments
VersionedBiobase Class "VersionedBiobase"
Versioned Class "Versioned"
data:geneData Sample expression matrix and phenotype data.frames.
reporter Example data.frame representing reporter information
featureNames Retrieve feature and sample names from eSets.
featureData Retrieve information on features recorded in eSet-derived classes.
data:sample.ExpressionSet Dataset of class 'ExpressionSet'
data:sample.MultiSet Data set of class 'MultiSet'
openVignette Open a Vignette or Show Vignette Selection Menu
openPDF Open PDF Files in a Standard Viewer
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
phenoData Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes.
package.version Report Version of a Package
updateObjectTo Update an object to the class definition of a template
testBioCConnection A function to check internet connectivity to Bioconductor
Aggregate A Simple Aggregation Mechanism.
annotatedDataFrameFrom-methods Methods for Function annotatedDataFrameFrom in Package `Biobase'
aggregator A Simple Class for Aggregators
AnnotatedDataFrame Class Containing Measured Variables and Their Meta-Data Description.
dims Retrieve dimensions of all elements in a list or environment
dumpPackTxt Dump Textual Description of a Package
isCurrent Use version information to test whether class is current
matchpt Nearest neighbor search.
multiassign Assign Values to a Names
reverseSplit A function to reverse the role of names and values in a list.
isUnique Determine Unique Elements
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
channel Create a new ExpressionSet instance by selecting a specific channel
channelNames Retrieve and set channel names from object
copyEnv List-Environment interactions
copySubstitute Copy Between Connections or Files with Configure-Like Name-Value Substitution
Deprecated and Defunct Biobase Deprecated and Defunct
description Retrieve and set overall experimental information eSet-like classes.
getPkgVigs List Vignette Files for a Package
Internals Internals
note Informational Messages
notes Retrieve and set eSet notes.
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.
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License Artistic-2.0
Collate tools.R strings.R environment.R vignettes.R packages.R AllGenerics.R VersionsClass.R VersionedClasses.R methods-VersionsNull.R methods-VersionedClass.R DataClasses.R methods-aggregator.R methods-container.R methods-MIAxE.R methods-MIAME.R methods-AssayData.R methods-AnnotatedDataFrame.R methods-eSet.R methods-ExpressionSet.R methods-MultiSet.R methods-SnpSet.R methods-NChannelSet.R anyMissing.R rowOp-methods.R updateObjectTo.R methods-ScalarObject.R zzz.R
LazyLoad yes
biocViews Infrastructure

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