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AnnotatedDataFrame Class Containing Measured Variables and Their
Meta-Data Description.
AssayData-class Class "AssayData"
Biobase-package Biobase Package Overview
ExpressionSet Class to Contain and Describe High-Throughput
Expression Level Assays.
MIAME Class for Storing Microarray Experiment
Information
MIAxE MIAxE objects
MultiSet Class to Contain and Describe High-Throughput
Expression Level Assays.
NChannelSet-class Class to contain data from multiple channel
array technologies
ScalarObject-class Utility classes for length one (scalar) objects
SnpSet Class to Contain Objects Describing
High-Throughput SNP Assays.
Versioned Class "Versioned"
VersionedBiobase Class "VersionedBiobase"
Versions Class "Versions"
VersionsNull Class "VersionsNull"
abstract Retrieve Meta-data from eSets and
ExpressionSets.
addVigs2WinMenu Add Menu Items to an Existing/New Menu of
Window
aggregator A Simple Class for Aggregators
annotatedDataFrameFrom
Methods for Function annotatedDataFrameFrom in
Package 'Biobase'
anyMissing Checks if there are any missing values in an
object or not
assayData Retrieve assay data from eSets and
ExpressionSets.
cache Evaluate an expression if its value is not
already cached.
channel Create a new ExpressionSet instance by
selecting a specific channel
channelNames Retrieve channel names from object
class:characterORMIAME
Class to Make Older Versions Compatible
classVersion Retrieve information about versioned classes
conditions Accessors and generic functions used in the
context of count datasets
container A Lockable List Structure with Constraints on
Content
contents Function to retrieve contents of environments
copyEnv List-Environment interactions
copySubstitute Copy Between Connections or Files with
Configure-Like Name-Value Substitution
createPackage Create a Package Directory from a Template
data:aaMap Dataset: Names and Characteristics of Amino
Acids
data:geneData Sample expression matrix and phenotype
data.frames.
data:sample.ExpressionSet
Dataset of class 'ExpressionSet'
data:sample.MultiSet Data set of class 'MultiSet'
description Retrieve and set overall experimental
information eSet-like classes.
dims Retrieve dimensions of all elements in a list
or environment
dumpPackTxt Dump Textual Description of a Package
eSet Class to Contain High-Throughput Assays and
Experimental Metadata
esApply An apply-like function for ExpressionSet and
related structures.
exprs Retrieve expression data from eSets.
featureData Retrieve information on features recorded in
eSet-derived classes.
featureNames Retrieve feature and sample names from eSets.
getPkgVigs List Vignette Files for a Package
isCurrent Use version information to test whether class
is current
isUnique Determine Unique Elements
isVersioned Determine whether object or class contains
versioning information
lcSuffix Compute the longest common prefix or suffix of
a string
listLen Lengths of list elements
makeDataPackage Make an R package from a data object
matchpt Nearest neighbor search.
multiassign Assign Values to a Names
note Informational Messages
notes Retrieve and set eSet notes.
openPDF Open PDF Files in a Standard Viewer
openVignette Open a Vignette or Show Vignette Selection Menu
package.version Report Version of a Package
phenoData Retrieve information on experimental phenotypes
recorded in eSet and ExpressionSet-derived
classes.
protocolData Protocol Metadata
read.AnnotatedDataFrame
Read 'AnnotatedDataFrame'
read.MIAME Read MIAME Information into an Instance of
Class 'MIAME'
readExpressionSet Read 'ExpressionSet'
reporter Example data.frame representing reporter
information
reverseSplit A function to reverse the role of names and
values in a list.
rowMedians Calculates the median for each row in a matrix
rowQ A function to compute empirical row quantiles.
selectChannels Create a new NChannelSet instance by selecting
specific channels
selectSome Extract elements of a vector for concise
rendering
snpCall Get and retrieve SNP call and call probability
data.
storageMode Retrieve or set storage mode for eSets.
strbreak Break Character Strings to Fit Width
subListExtract Extract the same element from the sublists of a
list
testBioCConnection A function to check internet connectivity to
Bioconductor
updateObjectTo Update an object to the class definition of a
template
updateOldESet Update previously created eSet object to
current eSet structure
userQuery A function to query the user for input
validMsg Conditionally append result to validity message
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