| aaMap |
Dataset: Names and Characteristics of Amino Acids |
| abstract |
Retrieve Meta-data from eSets and ExpressionSets. |
| abstract,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| abstract,MIAME-method |
Class for Storing Microarray Experiment Information |
| addVigs2WinMenu |
Add Menu Items to an Existing/New Menu of Window |
| aggenv,aggregator-method |
A Simple Class for Aggregators |
| aggfun,aggregator-method |
A Simple Class for Aggregators |
| Aggregate |
A Simple Aggregation Mechanism. |
| aggregator |
A Simple Class for Aggregators |
| aggregator-class |
A Simple Class for Aggregators |
| AnnotatedDataFrame |
Class Containing Measured Variables and Their Meta-Data Description. |
| AnnotatedDataFrame-class |
Class Containing Measured Variables and Their Meta-Data Description. |
| annotatedDataFrameFrom |
Methods for Function annotatedDataFrameFrom in Package ‘Biobase’ |
| annotatedDataFrameFrom,AssayData-method |
Methods for Function annotatedDataFrameFrom in Package ‘Biobase’ |
| annotatedDataFrameFrom,matrix-method |
Methods for Function annotatedDataFrameFrom in Package ‘Biobase’ |
| annotatedDataFrameFrom,NULL-method |
Methods for Function annotatedDataFrameFrom in Package ‘Biobase’ |
| annotation |
Annotate eSet data. |
| annotation,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| annotation<-,eSet,character-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| anyMissing |
Checks if there are any missing values in an object or not |
| as.data.frame.ExpressionSet |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| AssayData |
Class "AssayData" |
| assayData |
Retrieve assay data from eSets and ExpressionSets. |
| assayData,AssayData-method |
Class "AssayData" |
| assayData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| AssayData-class |
Class "AssayData" |
| assayData<-,eSet,AssayData-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| assayDataElement |
Class to Contain High-Throughput Assays and Experimental Metadata |
| assayDataElementNames |
Class to Contain High-Throughput Assays and Experimental Metadata |
| assayDataElementReplace |
Class to Contain High-Throughput Assays and Experimental Metadata |
| assayDataNew |
Class "AssayData" |
| assayDataValidMembers |
Class "AssayData" |
| cache |
Evaluate an expression if its value is not already cached. |
| channel |
Create a new ExpressionSet instance by selecting a specific channel |
| channel,NChannelSet,character-method |
Class to contain data from multiple channel array technologies |
| channelNames |
Retrieve channel names from object |
| channelNames,NChannelSet-method |
Class to contain data from multiple channel array technologies |
| characterORMIAME-class |
Class to Make Older Versions Compatible |
| class.NChannelSet |
Class to contain data from multiple channel array technologies |
| class:aggregator |
A Simple Class for Aggregators |
| class:AnnotatedDataFrame |
Class Containing Measured Variables and Their Meta-Data Description. |
| 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 Metadata |
| class:ExpressionSet |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| class:MIAME |
Class for Storing Microarray Experiment Information |
| class:MultiSet |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| class:SnpSet |
Class to Contain Objects Describing High-Throughput SNP Assays. |
| classVersion |
Retrieve information about versioned classes |
| classVersion,ANY-method |
Retrieve information about versioned classes |
| classVersion,character-method |
Retrieve information about versioned classes |
| classVersion,Versioned-method |
Class "Versioned" |
| classVersion<-,Versioned,Versions-method |
Class "Versioned" |
| coerce,data.frame,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| coerce,eSet,ExpressionSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| coerce,eSet,MultiSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| coerce,ExpressionSet,data.frame-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| coerce,exprSet,ExpressionSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| coerce,phenoData,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| coerce,Versions,character-method |
Class "Versions" |
| combine |
Methods for Function combine in Package ‘Biobase’ |
| combine,AnnotatedDataFrame,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| combine,ANY,missing-method |
Methods for Function combine in Package ‘Biobase’ |
| combine,AssayData,AssayData-method |
Class "AssayData" |
| combine,data.frame,data.frame-method |
Methods for Function combine in Package ‘Biobase’ |
| combine,eSet,ANY-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| combine,eSet,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| combine,matrix,matrix-method |
Methods for Function combine in Package ‘Biobase’ |
| combine,MIAME,MIAME-method |
Class for Storing Microarray Experiment Information |
| Compare,character,Versions-method |
Class "Versions" |
| Compare,Versions,character-method |
Class "Versions" |
| Compare,Versions,Versions-method |
Class "Versions" |
| container |
A Lockable List Structure with Constraints on Content |
| container-class |
A Lockable List Structure with Constraints on Content |
| content,container-method |
A Lockable List Structure with Constraints on Content |
| contents |
Function to retrieve contents of environments |
| copyEnv |
List-Environment interactions |
| copySubstitute |
Copy Between Connections or Files with Configure-Like Name-Value Substitution |
| createPackage |
Create a Package Directory from a Template |
| esApply |
An apply-like function for ExpressionSet and related structures. |
| esApply,ExpressionSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| eSet |
Class to Contain High-Throughput Assays and Experimental Metadata |
| eSet-class |
Class to Contain High-Throughput Assays and Experimental Metadata |
| experimentData |
Retrieve Meta-data from eSets and ExpressionSets. |
| experimentData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| experimentData<-,eSet,MIAME-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| expinfo,MIAME-method |
Class for Storing Microarray Experiment Information |
| ExpressionSet |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| ExpressionSet-class |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| exprs |
Retrieve expression data from eSets. |
| exprs,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| exprs,ExpressionSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| exprs,SnpSet-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |
| exprs<-,eSet,AssayData-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| exprs<-,ExpressionSet,matrix-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| exprs<-,SnpSet,matrix-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |
| fData |
Retrieve information on features recorded in eSet-derived classes. |
| fData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| fData<-,eSet,data.frame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| featureData |
Retrieve information on features recorded in eSet-derived classes. |
| featureData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| featureData<-,eSet,AnnotatedDataFrame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| featureNames |
Retrieve feature and sample names from eSets. |
| featureNames,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| featureNames,AssayData-method |
Class "AssayData" |
| featureNames,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| featureNames<-,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| featureNames<-,AssayData-method |
Class "AssayData" |
| featureNames<-,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| fvarLabels |
Retrieve information on features recorded in eSet-derived classes. |
| fvarLabels,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| fvarLabels<-,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| fvarMetadata |
Retrieve information on features recorded in eSet-derived classes. |
| fvarMetadata,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| fvarMetadata<-,eSet,data.frame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| initfun,aggregator-method |
A Simple Class for Aggregators |
| initialize,aggregator-method |
A Simple Class for Aggregators |
| initialize,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| initialize,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| initialize,ExpressionSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| initialize,MultiSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| initialize,NChannelSet-method |
Class to contain data from multiple channel array technologies |
| initialize,SnpSet-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |
| initialize,Versioned-method |
Class "Versioned" |
| initialize,Versions-method |
Class "Versions" |
| initialize,VersionsNull-method |
Class "VersionsNull" |
| isCurrent |
Use version information to test whether class is current |
| isCurrent,ANY,ANY-method |
Use version information to test whether class is current |
| isCurrent,MIAME,missing-method |
Class for Storing Microarray Experiment Information |
| isCurrent,Versioned,character-method |
Class "Versioned" |
| isCurrent,Versioned,missing-method |
Class "Versioned" |
| isUnique |
Determine Unique Elements |
| isVersioned |
Determine whether object or class contains versioning information |
| isVersioned,ANY-method |
Determine whether object or class contains versioning information |
| isVersioned,character-method |
Determine whether object or class contains versioning information |
| isVersioned,Versioned-method |
Class "Versioned" |
| NChannelSet |
Class to contain data from multiple channel array technologies |
| NChannelSet-class |
Class to contain data from multiple channel array technologies |
| ncol,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| ncol,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| normControls,MIAME-method |
Class for Storing Microarray Experiment Information |
| note |
Informational Messages |
| notes |
Retrieve and set eSet notes. |
| notes,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| notes,MIAME-method |
Class for Storing Microarray Experiment Information |
| notes<-,eSet,ANY-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| notes<-,MIAME,character-method |
Class for Storing Microarray Experiment Information |
| notes<-,MIAME,list-method |
Class for Storing Microarray Experiment Information |
| package.version |
Report Version of a Package |
| pData |
Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes. |
| pData,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| pData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| pData<-,AnnotatedDataFrame,data.frame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| pData<-,eSet,data.frame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| phenoData |
Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes. |
| phenoData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| phenoData<-,eSet,AnnotatedDataFrame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| preproc |
Class for Storing Microarray Experiment Information |
| preproc,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| preproc,MIAME-method |
Class for Storing Microarray Experiment Information |
| preproc<-,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| preproc<-,MIAME-method |
Class for Storing Microarray Experiment Information |
| pubMedIds |
Retrieve Meta-data from eSets and ExpressionSets. |
| pubMedIds,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| pubMedIds,MIAME-method |
Class for Storing Microarray Experiment Information |
| pubMedIds<-,eSet,character-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| pubMedIds<-,MIAME,ANY-method |
Class for Storing Microarray Experiment Information |
| sample.ExpressionSet |
Dataset of class 'ExpressionSet' |
| sample.MultiSet |
Data set of class 'MultiSet' |
| sampleNames |
Retrieve feature and sample names from eSets. |
| sampleNames,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| sampleNames,AssayData-method |
Class "AssayData" |
| sampleNames,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| sampleNames,NChannelSet-method |
Class to contain data from multiple channel array technologies |
| sampleNames<-,AnnotatedDataFrame,ANY-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| sampleNames<-,AssayData,ANY-method |
Class "AssayData" |
| sampleNames<-,AssayData,list-method |
Class "AssayData" |
| sampleNames<-,eSet,ANY-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| sampleNames<-,NChannelSet,list-method |
Class to contain data from multiple channel array technologies |
| samples |
Class for Storing Microarray Experiment Information |
| samples,MIAME-method |
Class for Storing Microarray Experiment Information |
| ScalarCharacter-class |
Utility classes for length one (scalar) objects |
| ScalarInteger-class |
Utility classes for length one (scalar) objects |
| ScalarNumeric-class |
Utility classes for length one (scalar) objects |
| ScalarObject-class |
Utility classes for length one (scalar) objects |
| se.exprs |
Retrieve expression data from eSets. |
| seD |
Sample expression matrix and phenotype data.frames. |
| selectChannels |
Create a new NChannelSet instance by selecting specific channels |
| selectChannels,NChannelSet,character-method |
Class to contain data from multiple channel array technologies |
| selectSome |
Extract elements of a vector for concise rendering |
| show,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| show,container-method |
A Lockable List Structure with Constraints on Content |
| show,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| show,MIAME-method |
Class for Storing Microarray Experiment Information |
| show,ScalarCharacter-method |
Utility classes for length one (scalar) objects |
| show,ScalarObject-method |
Utility classes for length one (scalar) objects |
| show,Versioned-method |
Class "Versioned" |
| show,Versions-method |
Class "Versions" |
| show,VersionsNull-method |
Class "VersionsNull" |
| SnpSet |
Class to Contain Objects Describing High-Throughput SNP Assays. |
| SnpSet-class |
Class to Contain Objects Describing High-Throughput SNP Assays. |
| storageMode |
Retrieve or set storage mode for eSets. |
| storageMode,AssayData-method |
Class "AssayData" |
| storageMode,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| storageMode<-,AssayData,character-method |
Class "AssayData" |
| storageMode<-,eSet,character-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| strbreak |
Break Character Strings to Fit Width |
| subListExtract |
Extract the same element from the sublists of a list |
| SW |
Class to Contain High-Throughput Assays and Experimental Metadata |
| updateObject |
Update an object to its current class definition |
| updateObject,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| updateObject,ANY-method |
Update an object to its current class definition |
| updateObject,environment-method |
Update an object to its current class definition |
| updateObject,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| updateObject,ExpressionSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
| updateObject,list-method |
Update an object to its current class definition |
| updateObject,MIAME-method |
Class for Storing Microarray Experiment Information |
| updateObject,Versions-method |
Class "Versions" |
| updateObjectFromSlots |
Update an object to its current class definition |
| updateObjectTo |
Update an object to its current class definition |
| updateObjectTo,ANY,ANY-method |
Update an object to its current class definition |
| updateObjectTo,eSet,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| updateOldESet |
Update previously created eSet object to current eSet structure |
| userQuery |
A function to query the user for input |
| validMsg |
Conditionally append result to validity message |
| varLabels |
Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes. |
| varLabels,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| varLabels,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| varLabels<-,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| varLabels<-,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| varMetadata |
Retrieve information on experimental phenotypes recorded in eSet and ExpressionSet-derived classes. |
| varMetadata,AnnotatedDataFrame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| varMetadata,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| varMetadata<-,AnnotatedDataFrame,data.frame-method |
Class Containing Measured Variables and Their Meta-Data Description. |
| varMetadata<-,eSet,data.frame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
| Versioned |
Class "Versioned" |
| Versioned-class |
Class "Versioned" |
| VersionedBiobase |
Class "VersionedBiobase" |
| VersionedBiobase-class |
Class "VersionedBiobase" |
| Versions |
Class "Versions" |
| Versions-class |
Class "Versions" |
| VersionsNull |
Class "VersionsNull" |
| VersionsNull-class |
Class "VersionsNull" |