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.
No Results!

Last year downloads

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

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/Biobase)](http://www.rdocumentation.org/packages/Biobase)