Biobase v2.30.0

Biobase: Base functions for Bioconductor

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

Functions in Biobase

Name Description
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
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Details

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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