Biobase: Biobase: Base functions for Bioconductor
Version 2.36.2

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

AuthorR. Gentleman, V. Carey, M. Morgan, S. Falcon
Bioconductor views Infrastructure
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version2.36.2
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Biobase")

Getting started

Package overview

Popular man pages

class.characterORmiame: Class to Make Older Versions Compatible
class.MultiSet: Class to Contain and Describe High-Throughput Expression...
data.sample.ExpressionSet: Dataset of class 'ExpressionSet'
featureData: Retrieve information on features recorded in eSet-derived...
listLen: Lengths of list elements
read.AnnotatedDataFrame: Read and write 'AnnotatedDataFrame'
snpCall: Get and retrieve SNP call and call probability data.
See all...

All man pages Function index File listing

Man pages

abstract: Retrieve Meta-data from eSets and ExpressionSets.
addVig2Menu: Add Menu Items to an Existing/New Menu of Window
Aggregate: A Simple Aggregation Mechanism.
annotatedDataFrameFrom-methods: Methods for Function annotatedDataFrameFrom in Package...
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.
channel: Create a new ExpressionSet instance by selecting a specific...
channelNames: Retrieve and set channel names from object
class.aggregator: A Simple Class for Aggregators
class.AnnotatedDataFrame: Class Containing Measured Variables and Their Meta-Data...
class.AssayData: Class "AssayData"
class.characterORmiame: Class to Make Older Versions Compatible
class.container: A Lockable List Structure with Constraints on Content
class.eSet: Class to Contain High-Throughput Assays and Experimental...
class.ExpressionSet: Class to Contain and Describe High-Throughput Expression...
class.MIAME: Class for Storing Microarray Experiment Information
class.MIAxE: MIAxE objects
class.MultiSet: Class to Contain and Describe High-Throughput Expression...
class.NChannelSet: Class to contain data from multiple channel array...
class.SnpSet: Class to Contain Objects Describing High-Throughput SNP...
classVersion: Retrieve information about versioned classes
class.Versioned: Class "Versioned"
class.VersionedBiobase: Class "VersionedBiobase"
class.Versions: Class "Versions"
class.VersionsNull: Class "VersionsNull"
contents: Function to retrieve contents of environments
copyEnv: List-Environment interactions
copySubstitute: Copy Between Connections or Files with Configure-Like...
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.reporter: Example data.frame representing reporter information
data.sample.ExpressionSet: Dataset of class 'ExpressionSet'
data.sample.MultiSet: Data set of class 'MultiSet'
defunct: Biobase Deprecated and Defunct
description: Retrieve and set overall experimental information eSet-like...
dims: Retrieve dimensions of all elements in a list or environment
dumpPackTxt: Dump Textual Description of a Package
esApply: An apply-like function for ExpressionSet and related...
exprs: Retrieve expression data from eSets.
featureData: Retrieve information on features recorded in eSet-derived...
featureNames: Retrieve feature and sample names from eSets.
getPkgVigs: List Vignette Files for a Package
internals: Internals
isCurrent: Use version information to test whether class is current
isUnique: Determine Unique Elements
isVersioned: Determine whether object or class contains versioning...
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...
protocolData: Protocol Metadata
read.AnnotatedDataFrame: Read and write 'AnnotatedDataFrame'
readExpressionSet: Read 'ExpressionSet'
read.MIAME: Read MIAME Information into an Instance of Class 'MIAME'
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.
ScalarObject-class: Utility classes for length one (scalar) objects
selectChannels: Create a new NChannelSet instance by selecting specific...
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...
userQuery: A function to query the user for input
validMsg: Conditionally append result to validity message

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/DataClasses.R
R/VersionedClasses.R
R/VersionsClass.R
R/anyMissing.R
R/environment.R
R/methods-AnnotatedDataFrame.R
R/methods-AssayData.R
R/methods-ExpressionSet.R
R/methods-MIAME.R
R/methods-MIAxE.R
R/methods-MultiSet.R
R/methods-NChannelSet.R
R/methods-ScalarObject.R
R/methods-SnpSet.R
R/methods-VersionedClass.R
R/methods-VersionsNull.R
R/methods-aggregator.R
R/methods-container.R
R/methods-eSet.R
R/packages.R
R/rowOp-methods.R
R/strings.R
R/tools.R
R/updateObjectTo.R
R/vignettes.R
R/zzz.R
build
build/vignette.rds
data
data/SW.rda
data/aaMap.R
data/geneCov.R
data/geneCovariate.rda
data/geneData.R
data/reporter.rda
data/sample.ExpressionSet.rda
data/sample.MultiSet.rda
data/sample.eSet.R
data/sample.exprSet.1.R
data/sample.exprSet.R
data/seD.rda
inst
inst/CITATION
inst/Code
inst/Code/DESCRIPTION
inst/Code/R
inst/Code/R/get@PKGNAME@.R
inst/Code/man
inst/Code/man/@PKGNAME@.Rd
inst/Code/man/get@PKGNAME@.Rd
inst/ExpressionSet
inst/ExpressionSet/DESCRIPTION
inst/ExpressionSet/man
inst/ExpressionSet/man/@PKGNAME@.Rd
inst/doc
inst/doc/BiobaseDevelopment.R
inst/doc/BiobaseDevelopment.Rnw
inst/doc/BiobaseDevelopment.pdf
inst/doc/ExpressionSetIntroduction.R
inst/doc/ExpressionSetIntroduction.Rnw
inst/doc/ExpressionSetIntroduction.pdf
inst/doc/esApply.R
inst/doc/esApply.Rnw
inst/doc/esApply.pdf
inst/extdata
inst/extdata/exprsData.txt
inst/extdata/pData.txt
inst/scripts
inst/scripts/esetTesting.R
inst/scripts/getBioC.R
inst/scripts/getBioCHelp
inst/scripts/getBioCPkgNames.R
inst/scripts/makeExpressionSetPackage.R
inst/scripts/query.packages.R
inst/testClass.R
inst/unitTests
inst/unitTests/VersionedClass_data
inst/unitTests/VersionedClass_data/1.8
inst/unitTests/VersionedClass_data/1.8/AnnotatedDataFrame.Rda
inst/unitTests/VersionedClass_data/1.8/ExpressionSet.Rda
inst/unitTests/VersionedClass_data/1.8/MIAME.Rda
inst/unitTests/VersionedClass_data/1.8/exprSet.Rda
inst/unitTests/VersionedClass_data/1.8/phenoData.Rda
inst/unitTests/VersionedClass_data/2.0
inst/unitTests/VersionedClass_data/2.0/AnnotatedDataFrame.Rda
inst/unitTests/VersionedClass_data/2.0/ExpressionSet.Rda
inst/unitTests/VersionedClass_data/2.0/MIAME.Rda
inst/unitTests/VersionedClass_data/2.0/MultiSet.Rda
inst/unitTests/VersionedClass_data/2.0/ScalarCharacter.Rda
inst/unitTests/VersionedClass_data/2.0/SnpSet.Rda
inst/unitTests/VersionedClass_data/2.0/Versioned.Rda
inst/unitTests/VersionedClass_data/2.0/VersionedBiobase.Rda
inst/unitTests/VersionedClass_data/2.0/Versions.Rda
inst/unitTests/VersionedClass_data/2.0/VersionsNull.Rda
inst/unitTests/VersionedClass_data/2.0/aggregator.Rda
inst/unitTests/VersionedClass_data/2.0/container.Rda
inst/unitTests/VersionedClass_data/2.0/exprSet.Rda
inst/unitTests/VersionedClass_data/2.0/phenoData.Rda
inst/unitTests/VersionedClass_data/devel
inst/unitTests/VersionedClass_data/devel/AnnotatedDataFrame.Rda
inst/unitTests/VersionedClass_data/devel/ExpressionSet.Rda
inst/unitTests/VersionedClass_data/devel/MIAME.Rda
inst/unitTests/VersionedClass_data/devel/MultiSet.Rda
inst/unitTests/VersionedClass_data/devel/NChannelSet.Rda
inst/unitTests/VersionedClass_data/devel/SWPD.rda
inst/unitTests/VersionedClass_data/devel/ScalarCharacter.Rda
inst/unitTests/VersionedClass_data/devel/ScalarInteger.Rda
inst/unitTests/VersionedClass_data/devel/ScalarLogical.Rda
inst/unitTests/VersionedClass_data/devel/ScalarNumeric.Rda
inst/unitTests/VersionedClass_data/devel/SnpSet.Rda
inst/unitTests/VersionedClass_data/devel/Versioned.Rda
inst/unitTests/VersionedClass_data/devel/VersionedBiobase.Rda
inst/unitTests/VersionedClass_data/devel/Versions.Rda
inst/unitTests/VersionedClass_data/devel/VersionsNull.Rda
inst/unitTests/VersionedClass_data/devel/aggregator.Rda
inst/unitTests/VersionedClass_data/devel/bbsym.rda
inst/unitTests/VersionedClass_data/devel/container.Rda
inst/unitTests/VersionedClass_data/devel/eset.rda
inst/unitTests/VersionedClass_data/devel/exprSet.Rda
inst/unitTests/VersionedClass_data/devel/golubMergeSub.rda
inst/unitTests/VersionedClass_data/devel/sample.eSet.rda
inst/unitTests/VersionedClass_data/devel/sample.exprSet.1.rda
inst/unitTests/VersionedClass_data/devel/sample.exprSet.rda
inst/unitTests/VersionedClass_data/devel/swrep.rda
inst/unitTests/VersionedClass_data/raw
inst/unitTests/VersionedClass_data/raw/exprs.tab
inst/unitTests/VersionedClass_data/raw/pData.tab
inst/unitTests/VersionedClass_data/raw/varMetadata.tab
inst/unitTests/test_AnnotatedDataFrame.R
inst/unitTests/test_AssayData.R
inst/unitTests/test_DataClasses.R
inst/unitTests/test_EsetSubclasses.R
inst/unitTests/test_ExpressionSet.R
inst/unitTests/test_NChannelSet.R
inst/unitTests/test_SnpSet.R
inst/unitTests/test_UpdateObject.R
inst/unitTests/test_VersionedClass.R
inst/unitTests/test_cache.R
inst/unitTests/test_checkClass.R
inst/unitTests/test_combine.R
inst/unitTests/test_copyEnv.R
inst/unitTests/test_esApply.R
inst/unitTests/test_subListExtract.R
inst/unitTests/test_unsaveSetSlot.R
inst/unitTests/utilities.R
man
man/Aggregate.Rd
man/Biobase-package.Rd
man/ScalarObject-class.Rd
man/abstract.Rd
man/addVig2Menu.Rd
man/annotatedDataFrameFrom-methods.Rd
man/anyMissing.Rd
man/assayData.Rd
man/cache.Rd
man/channel.Rd
man/channelNames.Rd
man/class.AnnotatedDataFrame.Rd
man/class.AssayData.Rd
man/class.ExpressionSet.Rd
man/class.MIAME.Rd
man/class.MIAxE.Rd
man/class.MultiSet.Rd
man/class.NChannelSet.Rd
man/class.SnpSet.Rd
man/class.Versioned.Rd
man/class.VersionedBiobase.Rd
man/class.Versions.Rd
man/class.VersionsNull.Rd
man/class.aggregator.Rd
man/class.characterORmiame.Rd
man/class.container.Rd
man/class.eSet.Rd
man/classVersion.Rd
man/contents.Rd
man/copyEnv.Rd
man/copySubstitute.Rd
man/createPackage.Rd
man/data.aaMap.Rd
man/data.geneData.Rd
man/data.reporter.Rd
man/data.sample.ExpressionSet.Rd
man/data.sample.MultiSet.Rd
man/defunct.Rd
man/description.Rd
man/dims.Rd
man/dumpPackTxt.Rd
man/esApply.Rd
man/exprs.Rd
man/featureData.Rd
man/featureNames.Rd
man/getPkgVigs.Rd
man/internals.Rd
man/isCurrent.Rd
man/isUnique.Rd
man/isVersioned.Rd
man/lcSuffix.Rd
man/listLen.Rd
man/makeDataPackage.Rd
man/matchpt.Rd
man/multiassign.Rd
man/note.Rd
man/notes.Rd
man/openPDF.Rd
man/openVignette.Rd
man/package.version.Rd
man/phenoData.Rd
man/protocolData.Rd
man/read.AnnotatedDataFrame.Rd
man/read.MIAME.Rd
man/readExpressionSet.Rd
man/reverseSplit.Rd
man/rowMedians.Rd
man/rowQ.Rd
man/selectChannels.Rd
man/selectSome.Rd
man/snpCall.Rd
man/storageMode.Rd
man/strbreak.Rd
man/subListExtract.Rd
man/testBioCConnection.Rd
man/updateObjectTo.Rd
man/updateOldESet.Rd
man/userQuery.Rd
man/validMsg.Rd
src
src/Rinit.c
src/anyMissing.c
src/envir.c
src/matchpt.c
src/rowMedians.c
src/rowMedians_TYPE-template.h
src/sublist_extract.c
src/templates-types.h
src/templates-types_undef.h
tests
tests/test-all.R
tests/test-rowMedians.R
vignettes
vignettes/BiobaseDevelopment.Rnw
vignettes/ExpressionSetIntroduction.Rnw
vignettes/esApply.Rnw
vignettes/legacy
vignettes/legacy/Biobase.Rnw
vignettes/legacy/Bioconductor.Rnw
vignettes/legacy/HowTo.Rnw
vignettes/legacy/Qviews.Rnw
Biobase documentation built on May 20, 2017, 9:54 p.m.

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