Biobase: Biobase: Base functions for Bioconductor

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

AuthorR. Gentleman, V. Carey, M. Morgan, S. Falcon
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version2.34.0

View on Bioconductor

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

Files in this package

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

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