Biobase v2.32.0

Biobase: Base functions for Bioconductor

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

Functions in Biobase

Name Description
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
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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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