$,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
$,annotatedDataset-method |
Virtual Superset for 'exprSet', 'eSet' etc. |
$,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
$,phenoData-method |
Class For Patient or Experiment Level Data |
$<-,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
$<-,annotatedDataset-method |
Virtual Superset for 'exprSet', 'eSet' etc. |
$<-,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
$<-,phenoData-method |
Class For Patient or Experiment Level Data |
aaMap |
Dataset: Names and Characteristics of Amino Acids |
abstract |
Retrieve feature and sample names from eSets and exprSets. |
abstract,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
abstract,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
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 to Contain Measured Variables and Their Meta-Data Description. |
AnnotatedDataFrame-class |
Class to Contain Measured Variables and Their Meta-Data Description. |
annotatedDataset |
Virtual Superset for 'exprSet', 'eSet' etc. |
annotatedDataset-class |
Virtual Superset for 'exprSet', 'eSet' etc. |
annotation |
Annotate eSet data. |
annotation,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
annotation,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
annotation<-,eSet,character-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
annotation<-,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
as.data.frame.exprSet |
Class for Microarray Data and Methods for Processing Them |
as.data.frame.exprSet,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
AssayData |
Class "AssayData" |
assayData |
Retrieve assay data from eSets and exprSets. |
assayData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
assayData,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
AssayData-class |
Class "AssayData" |
assayData<-,eSet,AssayData-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
assayDataElement |
Class "AssayData" |
assayDataElementNames |
Class "AssayData" |
assayDataElementReplace |
Class "AssayData" |
assayDataNew |
Class "AssayData" |
assayDataValidMembers |
Class "AssayData" |
cache |
Evaluate an expression if its value is not already cached. |
characterORMIAME-class |
Class to Make Older Versions Compatible |
class:aggregator |
A Simple Class for Aggregators |
class:AnnotatedDataFrame |
Class to Contain Measured Variables and Their Meta-Data Description. |
class:annotatedDataset |
Virtual Superset for 'exprSet', 'eSet' etc. |
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:exprList |
Class Union of a List and an Environment |
class:exprMatrix |
Class Union for Objects Behaving Like a Matrix |
class:exprSet |
Class for Microarray Data and Methods for Processing Them |
class:MIAME |
Class for Storing Microarray Experiment Information |
class:MultiSet |
Class to Contain and Describe High-Throughput Expression Level Assays. |
class:phenoData |
Class For Patient or Experiment Level Data |
class:SnpSet |
Class to Contain Objects Describing High-Throughput SNP Assays. |
coerce,data.frame,phenoData-method |
Class For Patient or Experiment Level Data |
coerce,exprSet,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
coerce,exprSet,ExpressionSet-method |
Class to Contain and Describe High-Throughput Expression Level Assays. |
coerce,phenoData,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
combine |
Combine Data Into a Single Object. |
combine,AnnotatedDataFrame,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
combine,AssayData,AssayData-method |
Class "AssayData" |
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,MIAME,MIAME-method |
Class for Storing Microarray Experiment Information |
combine,phenoData,ANY-method |
Class For Patient or Experiment Level Data |
combine,phenoData,phenoData-method |
Class For Patient or Experiment Level Data |
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 |
convertVarLabels,phenoData-method |
Class For Patient or Experiment Level Data |
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 |
Apply for the Expression Data in 'exprSet' |
eSet |
Class to Contain High-Throughput Assays and Experimental Metadata |
eset |
(Deprecated) dataset of class 'exprSet' |
eSet-class |
Class to Contain High-Throughput Assays and Experimental Metadata |
experimentData |
Retrieve feature and sample names from eSets and exprSets. |
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. |
exprMatrix-class |
Class Union for Objects Behaving Like a Matrix |
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,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
exprs,SnpSet-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |
exprs2excel |
Class for Microarray Data and Methods for Processing Them |
exprs2excel,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
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<-,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
exprs<-,SnpSet,matrix-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |
exprSet |
Class for Microarray Data and Methods for Processing Them |
exprSet-class |
Class for Microarray Data and Methods for Processing Them |
geneCovariate |
A subset of some expression data. |
geneData |
A subset of some expression data. |
geneNames |
Retrieve feature and sample names from eSets and exprSets. |
geneNames,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
geneNames<-,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
getExpData,eSet,character-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
getPkgVigs |
List Vignette Files for a Package |
getVarMetadata |
Class For Patient or Experiment Level Data |
getVarMetadata,phenoData,character,character-method |
Class For Patient or Experiment Level Data |
getVarMetadata,phenoData,character,missing-method |
Class For Patient or Experiment Level Data |
golubMergeSub |
Class to Contain High-Throughput Assays and Experimental Metadata |
initfun,aggregator-method |
A Simple Class for Aggregators |
initialize,AnnotatedDataFrame-method |
Class to Contain 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,SnpSet-method |
Class to Contain Objects Describing High-Throughput SNP Assays. |
isUnique |
Determine Unique Elements |
iter,exprSet,character,function-method |
Class for Microarray Data and Methods for Processing Them |
iter,exprSet,missing,function-method |
Class for Microarray Data and Methods for Processing Them |
iter,exprSet,missing,list-method |
Class for Microarray Data and Methods for Processing Them |
ncol,AnnotatedDataFrame-method |
Class to Contain 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 and exprSet notes. |
notes,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
notes,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
notes,MIAME-method |
Class for Storing Microarray Experiment Information |
notes<-,eSet,list-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
notes<-,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
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 exprSet-derived classes. |
pData,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
pData,annotatedDataset-method |
Virtual Superset for 'exprSet', 'eSet' etc. |
pData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
pData,phenoData-method |
Class For Patient or Experiment Level Data |
pData<-,AnnotatedDataFrame,data.frame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
pData<-,annotatedDataset,ANY-method |
Virtual Superset for 'exprSet', 'eSet' etc. |
pData<-,eSet,data.frame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
pData<-,phenoData,ANY-method |
Class For Patient or Experiment Level Data |
phenoData |
Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes. |
phenoData,annotatedDataset-method |
Virtual Superset for 'exprSet', 'eSet' etc. |
phenoData,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
phenoData-class |
Class For Patient or Experiment Level Data |
phenoData<-,annotatedDataset,phenoData-method |
Class For Patient or Experiment Level Data |
phenoData<-,eSet,AnnotatedDataFrame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
preproc,MIAME-method |
Class for Storing Microarray Experiment Information |
pubMedIds |
Retrieve feature and sample names from eSets and exprSets. |
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.eSet |
Dataset of class 'eSet' |
sample.ExpressionSet |
Dataset of class 'ExpressionSet' |
sample.exprSet |
Dataset of class 'exprSet' |
sample.exprSet.1 |
Dataset of class 'exprSet' |
sampleNames |
Retrieve feature and sample names from eSets and exprSets. |
sampleNames,AnnotatedDataFrame-method |
Class to Contain 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,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
sampleNames<-,AnnotatedDataFrame-method |
Class to Contain 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<-,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
samples |
Class for Storing Microarray Experiment Information |
samples,MIAME-method |
Class for Storing Microarray Experiment Information |
se.exprs |
Retrieve expression data from eSets. |
se.exprs,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
se.exprs<-,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
seD |
A subset of some expression data. |
show,AnnotatedDataFrame-method |
Class to Contain 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,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
show,MIAME-method |
Class for Storing Microarray Experiment Information |
show,phenoData-method |
Class For Patient or Experiment Level Data |
SnpSet |
Class to Contain Objects Describing High-Throughput SNP Assays. |
SnpSet-class |
Class to Contain Objects Describing High-Throughput SNP Assays. |
split |
Class for Microarray Data and Methods for Processing Them |
split,exprSet,factor,missing-method |
Class for Microarray Data and Methods for Processing Them |
split,exprSet,vector,missing-method |
Class for Microarray Data and Methods for Processing Them |
split,phenoData,vector,missing-method |
Class For Patient or Experiment Level Data |
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 |
SW |
Class to Contain High-Throughput Assays and Experimental Metadata |
SWPD |
Class to Contain High-Throughput Assays and Experimental Metadata |
swrep |
Class to Contain High-Throughput Assays and Experimental Metadata |
varLabels |
Retrieve information on experimental phenotypes recorded in eSet and exprSet-derived classes. |
varLabels,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
varLabels,annotatedDataset-method |
Virtual Superset for 'exprSet', 'eSet' etc. |
varLabels,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
varLabels,phenoData-method |
Class For Patient or Experiment Level Data |
varLabels<-,AnnotatedDataFrame-method |
Class to Contain 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 exprSet-derived classes. |
varMetadata,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
varMetadata,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
varMetadata,phenoData-method |
Class For Patient or Experiment Level Data |
varMetadata<-,AnnotatedDataFrame,data.frame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
varMetadata<-,eSet,data.frame-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
[,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
[,container-method |
A Lockable List Structure with Constraints on Content |
[,eSet-method |
Class to Contain High-Throughput Assays and Experimental Metadata |
[,exprSet-method |
Class for Microarray Data and Methods for Processing Them |
[,phenoData-method |
Class For Patient or Experiment Level Data |
[[,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
[[,annotatedDataset-method |
Virtual Superset for 'exprSet', 'eSet' etc. |
[[,container-method |
A Lockable List Structure with Constraints on Content |
[[,phenoData-method |
Class For Patient or Experiment Level Data |
[[<-,AnnotatedDataFrame-method |
Class to Contain Measured Variables and Their Meta-Data Description. |
[[<-,annotatedDataset-method |
Virtual Superset for 'exprSet', 'eSet' etc. |
[[<-,container-method |
A Lockable List Structure with Constraints on Content |
[[<-,phenoData-method |
Class For Patient or Experiment Level Data |