Package: Biobase 2.65.0
Bioconductor Package Maintainer
Biobase: Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
Authors:
Biobase_2.65.0.tar.gz
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Biobase.pdf |Biobase.html✨
Biobase/json (API)
NEWS
| # Install 'Biobase' in R: |
| install.packages('Biobase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/biobase/issues
Datasets:
- SW - Class to Contain High-Throughput Assays and Experimental Metadata
- aaMap - Dataset: Names and Characteristics of Amino Acids
- geneCov - Sample expression matrix and phenotype data.frames.
- geneCovariate - Sample expression matrix and phenotype data.frames.
- geneData - Sample expression matrix and phenotype data.frames.
- reporter - Example data.frame representing reporter information
- sample.ExpressionSet - Dataset of class 'ExpressionSet'
- sample.MultiSet - Data set of class 'MultiSet'
- seD - Sample expression matrix and phenotype data.frames.
On BioConductor:Biobase-2.65.0(bioc 3.20)Biobase-2.64.0(bioc 3.19)
Last updated 2 months agofrom:a613de84b8
Exports:abstractaddVigs2WinMenuaggenvaggfunAggregateAnnotatedDataFrameannotatedDataFrameFromannotationannotation<-anyMissingas.data.frame.ExpressionSetassayDataassayData<-assayDataElementassayDataElement<-assayDataElementNamesassayDataElementReplaceassayDataNewassayDataValidMemberscachechannelchannelNameschannelNames<-classVersionclassVersion<-coercecombineComparecontentcontentscopyEnvcopySubstitutecreatePackagedescriptiondescription<-dimLabelsdimLabels<-dimsdumpPackTxtesApplyexperimentDataexperimentData<-expinfoExpressionSetexprsexprs<-fDatafData<-featureDatafeatureData<-featureNamesfeatureNames<-fvarLabelsfvarLabels<-fvarMetadatafvarMetadata<-getPkgVigshybridizationsinitfuninitializeisCurrentisUniqueisVersionedlcPrefixlcPrefixClcSuffixlistLenlockedmakeDataPackagematchptMIAMEmkScalarmultiassignNChannelSetnormControlsnotenotesnotes<-openPDFopenVignetteotherInfopackage.versionpDatapData<-phenoDataphenoData<-preprocpreproc<-protocolDataprotocolData<-pubMedIdspubMedIds<-read.AnnotatedDataFrameread.MIAMEreadExpressionSetreverseSplitrowMaxrowMediansrowMinrowQsampleNamessampleNames<-samplesse.exprsse.exprs<-selectChannelsselectSomeshowsnpCallsnpCall<-snpCallProbabilitysnpCallProbability<-storageModestorageMode<-strbreaksubListExtracttestBioCConnectionupdateObjectupdateObjectToupdateOldESetuserQueryvalidMsgvarLabelsvarLabels<-varMetadatavarMetadata<-write.AnnotatedDataFramewrite.exprs
Dependencies:BiocGenerics
An introduction to Biobase and ExpressionSets
Rendered fromExpressionSetIntroduction.Rnwusingutils::Sweaveon Jun 11 2024.Last update: 2018-07-17
Started: 2013-10-18
esApply Introduction
Rendered fromesApply.Rmdusingknitr::rmarkdownon Jun 11 2024.Last update: 2022-10-28
Started: 2022-10-22
Biobase development and the new eSet
Rendered fromBiobaseDevelopment.Rmdusingknitr::rmarkdownon Jun 11 2024.Last update: 2022-10-31
Started: 2022-10-31
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Biobase Package Overview | Biobase-package Biobase |
| Retrieve Meta-data from eSets and ExpressionSets. | abstract experimentData experimentData<- pubMedIds pubMedIds<- |
| Add Menu Items to an Existing/New Menu of Window | addVigs2WinMenu |
| A Simple Aggregation Mechanism. | Aggregate |
| A Simple Class for Aggregators | aggenv,aggregator-method aggfun,aggregator-method aggregator aggregator-class class:aggregator initfun,aggregator-method initialize,aggregator-method |
| Class Containing Measured Variables and Their Meta-Data Description. | $,AnnotatedDataFrame-method $<-,AnnotatedDataFrame-method AnnotatedDataFrame AnnotatedDataFrame,data.frame,data.frame-method AnnotatedDataFrame,data.frame,missing-method AnnotatedDataFrame,missing,missing-method AnnotatedDataFrame-class class:AnnotatedDataFrame coerce,AnnotatedDataFrame,data.frame-method coerce,data.frame,AnnotatedDataFrame-method coerce,phenoData,AnnotatedDataFrame-method combine,AnnotatedDataFrame,AnnotatedDataFrame-method dim,AnnotatedDataFrame-method dimLabels dimLabels,AnnotatedDataFrame-method dimLabels<- dimLabels<-,AnnotatedDataFrame,character-method dimnames,AnnotatedDataFrame-method dimnames<-,AnnotatedDataFrame-method featureNames,AnnotatedDataFrame-method featureNames<-,AnnotatedDataFrame-method head.AnnotatedDataFrame initialize,AnnotatedDataFrame-method ncol,AnnotatedDataFrame-method pData,AnnotatedDataFrame-method pData<-,AnnotatedDataFrame,data.frame-method sampleNames,AnnotatedDataFrame-method sampleNames<-,AnnotatedDataFrame,ANY-method show,AnnotatedDataFrame-method tail.AnnotatedDataFrame updateObject,AnnotatedDataFrame-method varLabels,AnnotatedDataFrame-method varLabels<-,AnnotatedDataFrame-method varMetadata,AnnotatedDataFrame-method varMetadata<-,AnnotatedDataFrame,data.frame-method [,AnnotatedDataFrame-method [[,AnnotatedDataFrame-method [[<-,AnnotatedDataFrame-method |
| Methods for Function annotatedDataFrameFrom in Package `Biobase' | annotatedDataFrameFrom annotatedDataFrameFrom,AssayData-method annotatedDataFrameFrom,matrix-method annotatedDataFrameFrom,NULL-method |
| Checks if there are any missing values in an object or not | anyMissing |
| Retrieve assay data from eSets and ExpressionSets. | assayData assayData<- |
| Class "AssayData" | AssayData assayData,AssayData-method AssayData-class assayDataNew assayDataValidMembers combine,AssayData,AssayData-method featureNames,AssayData-method featureNames<-,AssayData-method sampleNames,AssayData-method sampleNames<-,AssayData,ANY-method sampleNames<-,AssayData,list-method storageMode,AssayData-method storageMode<-,AssayData,character-method |
| Evaluate an expression if its value is not already cached. | cache |
| Create a new ExpressionSet instance by selecting a specific channel | channel |
| Retrieve and set channel names from object | channelNames channelNames<- |
| Class to Make Older Versions Compatible | characterORMIAME-class class:characterORMIAME |
| Retrieve information about versioned classes | classVersion classVersion,ANY-method classVersion,character-method classVersion<- |
| A Lockable List Structure with Constraints on Content | class:container container container-class content,container-method length,container-method locked,container-method show,container-method [,container-method [[,container-method [[<-,container-method |
| Function to retrieve contents of environments | contents |
| List-Environment interactions | copyEnv |
| Copy Between Connections or Files with Configure-Like Name-Value Substitution | copySubstitute |
| Create a Package Directory from a Template | createPackage |
| Dataset: Names and Characteristics of Amino Acids | aaMap data:aaMap |
| Sample expression matrix and phenotype data.frames. | data:geneCov data:geneCovariate data:geneData data:seD geneCov geneCovariate geneData seD |
| Dataset of class 'ExpressionSet' | data:sample.ExpressionSet sample.ExpressionSet |
| Data set of class 'MultiSet' | data:sample.MultiSet sample.MultiSet |
| Retrieve and set overall experimental information eSet-like classes. | description description<- |
| Dump Textual Description of a Package | dumpPackTxt |
| An apply-like function for ExpressionSet and related structures. | esApply |
| Class to Contain High-Throughput Assays and Experimental Metadata | $,eSet-method $<-,eSet-method abstract,eSet-method annotation,eSet-method annotation<-,eSet,character-method assayData,eSet-method assayData<-,eSet,AssayData-method assayDataElement assayDataElement<- assayDataElementNames assayDataElementReplace class:eSet combine,eSet,ANY-method combine,eSet,eSet-method description,eSet-method description<-,eSet,MIAME-method dim,eSet-method dimnames dimnames,eSet-method dimnames<- dimnames<-,eSet-method dims dims,eSet-method eSet eSet-class experimentData,eSet-method experimentData<-,eSet,MIAME-method exprs,eSet-method exprs<-,eSet,AssayData-method fData,eSet-method fData<-,eSet,data.frame-method featureData,eSet-method featureData<-,eSet,AnnotatedDataFrame-method featureNames,eSet-method featureNames<-,eSet-method fvarLabels,eSet-method fvarLabels<-,eSet-method fvarMetadata,eSet-method fvarMetadata<-,eSet,data.frame-method initialize,eSet-method listOrEnv ncol,eSet-method notes,eSet-method notes<-,eSet,ANY-method pData,eSet-method pData<-,eSet,data.frame-method phenoData,eSet-method phenoData<-,eSet,AnnotatedDataFrame-method preproc,eSet-method preproc<-,eSet-method protocolData,eSet-method protocolData<-,eSet,character-method pubMedIds,eSet-method pubMedIds<-,eSet,character-method sampleNames,eSet-method sampleNames<-,eSet,ANY-method show,eSet-method storageMode,eSet-method storageMode<-,eSet,character-method SW updateObject,eSet-method updateObjectTo,eSet,eSet-method varLabels,eSet-method varLabels<-,eSet-method varMetadata,eSet-method varMetadata<-,eSet,data.frame-method [,eSet-method [[,eSet-method [[<-,eSet-method |
| Class to Contain and Describe High-Throughput Expression Level Assays. | as.data.frame.ExpressionSet class:ExpressionSet coerce,eSet,ExpressionSet-method coerce,ExpressionSet,data.frame-method coerce,exprSet,ExpressionSet-method esApply,ExpressionSet-method ExpressionSet ExpressionSet,environment-method ExpressionSet,matrix-method ExpressionSet,missing-method ExpressionSet-class exprs,ExpressionSet-method exprs<-,ExpressionSet,matrix-method initialize,ExpressionSet-method makeDataPackage,ExpressionSet-method updateObject,ExpressionSet-method write.exprs write.exprs,ExpressionSet-method |
| Retrieve expression data from eSets. | exprs exprs<- se.exprs se.exprs<- |
| Retrieve information on features recorded in eSet-derived classes. | fData fData<- featureData featureData<- fvarLabels fvarLabels<- fvarMetadata fvarMetadata<- |
| Retrieve feature and sample names from eSets. | featureNames featureNames<- sampleNames sampleNames<- |
| List Vignette Files for a Package | getPkgVigs |
| Use version information to test whether class is current | isCurrent isCurrent,ANY,ANY-method |
| Determine Unique Elements | isUnique |
| Determine whether object or class contains versioning information | isVersioned isVersioned,ANY-method isVersioned,character-method |
| Compute the longest common prefix or suffix of a string | lcPrefix lcPrefixC lcSuffix |
| Lengths of list elements | listLen |
| Make an R package from a data object | makeDataPackage makeDataPackage,ANY-method |
| Nearest neighbor search. | matchpt |
| Class for Storing Microarray Experiment Information | abstract,MIAME-method class:MIAME combine,MIAME,MIAME-method expinfo,MIAME-method hybridizations,MIAME-method isCurrent,MIAME,missing-method MIAME MIAME-class normControls,MIAME-method notes,MIAME-method notes<-,MIAME,character-method notes<-,MIAME,list-method otherInfo,MIAME-method preproc preproc,MIAME-method preproc<- preproc<-,MIAME-method pubMedIds,MIAME-method pubMedIds<-,MIAME,ANY-method samples samples,MIAME-method show,MIAME-method updateObject,MIAME-method |
| MIAxE objects | class:MIAxE MIAxE MIAxE-class show,MIAxE-method |
| Assign Values to a Names | multiassign |
| Class to Contain and Describe High-Throughput Expression Level Assays. | class:MultiSet coerce,eSet,MultiSet-method initialize,MultiSet-method MultiSet MultiSet-class |
| Class to contain data from multiple channel array technologies | assayData<-,NChannelSet,environment-method assayData<-,NChannelSet,list-method channel,NChannelSet,character-method channelNames,NChannelSet-method channelNames<-,NChannelSet,character-method channelNames<-,NChannelSet,list-method class.NChannelSet initialize,NChannelSet-method NChannelSet NChannelSet-class sampleNames,NChannelSet-method sampleNames<-,NChannelSet,list-method selectChannels,NChannelSet,character-method |
| Informational Messages | note |
| Retrieve and set eSet notes. | notes notes<- |
| Open PDF Files in a Standard Viewer | openPDF |
| Open a Vignette or Show Vignette Selection Menu | openVignette |
| Report Version of a Package | package.version |
| Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes. | pData pData<- phenoData phenoData<- varLabels varLabels<- varMetadata varMetadata<- |
| Protocol Metadata | protocolData protocolData<- protocolData<-,eSet,AnnotatedDataFrame-method |
| Read and write 'AnnotatedDataFrame' | read.AnnotatedDataFrame write.AnnotatedDataFrame |
| Read MIAME Information into an Instance of Class 'MIAME' | read.MIAME |
| Read 'ExpressionSet' | readExpressionSet |
| Example data.frame representing reporter information | data:reporter reporter |
| A function to reverse the role of names and values in a list. | reverseSplit |
| Calculates the median for each row in a matrix | rowMedians rowMedians,ExpressionSet-method rowMedians,matrix-method |
| A function to compute empirical row quantiles. | rowMax rowMin rowQ rowQ,ExpressionSet,numeric-method rowQ,matrix,numeric-method |
| Utility classes for length one (scalar) objects | mkScalar ScalarCharacter-class ScalarInteger-class ScalarLogical-class ScalarNumeric-class ScalarObject-class show,ScalarCharacter-method show,ScalarObject-method |
| Create a new NChannelSet instance by selecting specific channels | selectChannels |
| Extract elements of a vector for concise rendering | selectSome |
| Get and retrieve SNP call and call probability data. | snpCall snpCall<- snpCallProbability snpCallProbability<- |
| Class to Contain Objects Describing High-Throughput SNP Assays. | class:SnpSet exprs,SnpSet-method exprs<-,SnpSet,matrix-method initialize,SnpSet-method snpCall,SnpSet-method snpCall<-,SnpSet,matrix-method snpCallProbability,SnpSet-method snpCallProbability<-,SnpSet,matrix-method SnpSet SnpSet-class |
| Retrieve or set storage mode for eSets. | storageMode storageMode<- |
| Break Character Strings to Fit Width | strbreak |
| Extract the same element from the sublists of a list | subListExtract |
| A function to check internet connectivity to Bioconductor | testBioCConnection |
| Update an object to the class definition of a template | updateObjectTo updateObjectTo,ANY,ANY-method |
| Update previously created eSet object to current eSet structure | updateOldESet |
| A function to query the user for input | userQuery |
| Conditionally append result to validity message | validMsg |
| Class "Versioned" | classVersion,Versioned-method classVersion<-,Versioned,Versions-method initialize,Versioned-method isCurrent,Versioned,character-method isCurrent,Versioned,missing-method isVersioned,Versioned-method show,Versioned-method Versioned Versioned-class |
| Class "VersionedBiobase" | VersionedBiobase VersionedBiobase-class |
| Class "Versions" | $<-,Versions-method coerce,Versions,character-method Compare,character,Versions-method Compare,Versions,character-method Compare,Versions,Versions-method initialize,Versions-method show,Versions-method updateObject,Versions-method Versions Versions-class [,Versions-method [<-,Versions-method [[<-,Versions-method |
| Class "VersionsNull" | initialize,VersionsNull-method show,VersionsNull-method VersionsNull VersionsNull-class |
