Biobase: Biobase: Base functions for Bioconductor

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

Author
R. Gentleman, V. Carey, M. Morgan, S. Falcon
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
2.34.0

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