Biobase v2.26.0

Biobase: Base functions for Bioconductor

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

Functions in Biobase

Name Description
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.
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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
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