| Biobase-package |
Biobase Package Overview |
| data:sample.MultiSet |
Data set of class 'MultiSet' |
| selectChannels |
Create a new NChannelSet instance by selecting specific channels |
| exprs |
Retrieve expression data from eSets. |
| esApply |
An apply-like function for ExpressionSet and related structures.
|
| selectSome |
Extract elements of a vector for concise rendering |
| validMsg |
Conditionally append result to validity message |
| Versions |
Class "Versions" |
| MIAxE |
MIAxE objects |
| VersionsNull |
Class "VersionsNull" |
| cache |
Evaluate an expression if its value is not already cached. |
| data:sample.ExpressionSet |
Dataset of class 'ExpressionSet' |
| MultiSet |
Class to Contain and Describe High-Throughput Expression Level Assays.
|
| channelNames |
Retrieve and set channel names from object |
| channel |
Create a new ExpressionSet instance by selecting a specific channel |
| aggregator |
A Simple Class for Aggregators |
| annotatedDataFrameFrom-methods |
Methods for Function annotatedDataFrameFrom in Package `Biobase' |
| Aggregate |
A Simple Aggregation Mechanism. |
| ExpressionSet |
Class to Contain and Describe High-Throughput Expression Level Assays.
|
| MIAME |
Class for Storing Microarray Experiment Information
|
| SnpSet |
Class to Contain Objects Describing High-Throughput SNP Assays.
|
| Deprecated and Defunct |
Biobase Deprecated and Defunct |
| NChannelSet-class |
Class to contain data from multiple channel array technologies |
| description |
Retrieve and set overall experimental information eSet-like classes. |
| getPkgVigs |
List Vignette Files for a Package |
| Internals |
Internals |
| listLen |
Lengths of list elements |
| protocolData |
Protocol Metadata |
| read.AnnotatedDataFrame |
Read and write 'AnnotatedDataFrame' |
| makeDataPackage |
Make an R package from a data object |
| AnnotatedDataFrame |
Class Containing Measured Variables and Their Meta-Data Description.
|
| data:geneData |
Sample expression matrix and phenotype data.frames. |
| featureData |
Retrieve information on features recorded in eSet-derived
classes. |
| reporter |
Example data.frame representing reporter information |
| featureNames |
Retrieve feature and sample names from eSets. |
| note |
Informational Messages |
| notes |
Retrieve and set eSet notes. |
| ScalarObject-class |
Utility classes for length one (scalar) objects |
| rowQ |
A function to compute empirical row quantiles. |
| snpCall |
Get and retrieve SNP call and call probability data. |
| storageMode |
Retrieve or set storage mode for eSets. |
| abstract |
Retrieve Meta-data from eSets and ExpressionSets. |
| addVigs2WinMenu |
Add Menu Items to an Existing/New Menu of Window |
| container |
A Lockable List Structure with Constraints on Content |
| AssayData-class |
Class "AssayData" |
| class:characterORMIAME |
Class to Make Older Versions Compatible |
| copyEnv |
List-Environment interactions |
| copySubstitute |
Copy Between Connections or Files with Configure-Like Name-Value Substitution |
| isUnique |
Determine Unique Elements |
| isCurrent |
Use version information to test whether class is current |
| openPDF |
Open PDF Files in a Standard Viewer |
| openVignette |
Open a Vignette or Show Vignette Selection Menu |
| read.MIAME |
Read MIAME Information into an Instance of Class 'MIAME'
|
| readExpressionSet |
Read 'ExpressionSet' |
| strbreak |
Break Character Strings to Fit Width |
| subListExtract |
Extract the same element from the sublists of a list |
| Versioned |
Class "Versioned" |
| eSet |
Class to Contain High-Throughput Assays and Experimental Metadata
|
| createPackage |
Create a Package Directory from a Template |
| VersionedBiobase |
Class "VersionedBiobase" |
| data:aaMap |
Dataset: Names and Characteristics of Amino Acids |
| isVersioned |
Determine whether object or class contains versioning information |
| lcSuffix |
Compute the longest common prefix or suffix of a string |
| package.version |
Report Version of a Package |
| phenoData |
Retrieve information on experimental phenotypes recorded in
eSet and ExpressionSet-derived classes. |
| reverseSplit |
A function to reverse the role of names and values in a list. |
| rowMedians |
Calculates the median for each row in a matrix |
| updateOldESet |
Update previously created eSet object to current eSet structure |
| userQuery |
A function to query the user for input |
| anyMissing |
Checks if there are any missing values in an object or not |
| assayData |
Retrieve assay data from eSets and ExpressionSets. |
| classVersion |
Retrieve information about versioned classes |
| contents |
Function to retrieve contents of environments |
| dims |
Retrieve dimensions of all elements in a list or environment |
| dumpPackTxt |
Dump Textual Description of a Package |
| multiassign |
Assign Values to a Names |
| matchpt |
Nearest neighbor search. |
| testBioCConnection |
A function to check internet connectivity to Bioconductor |
| updateObjectTo |
Update an object to the class definition of a template |
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