Biobase: Base functions for Bioconductor


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Documentation for package `Biobase' version 1.8.0

User Guides and Package Vignettes

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A B C D E G L M N O P R S T U V W

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Biobase-package Biobase Package Overview

-- A --

aaMap Dataset: Names and Characteristics of Amino Acids
addVigs2WinMenu Add Menu Items to an Existing/New Menu of Window
Aggregate A Simple Aggregation Mechanism.
aggregator A Simple Class for Aggregators
annotatedDataset Virtual Superset for 'exprSet', 'eSet' etc.
as.data.frame.exprSet Class for Microarray Data and Methods for Processing Them
assayData General Container for High-Throughput Assays and Experimental Metadata

-- B --

Biobase Biobase Package Overview

-- C --

class:aggregator A Simple Class for Aggregators
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 General Container for High-Throughput Assays and Experimental Metadata
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:phenoData Class For Patient or Experiment Level Data
combine Combine Data Into a Single Object.
container 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

-- D --

data:aaMap Dataset: Names and Characteristics of Amino Acids
data:eset Dataset of class 'exprSet'
data:exSet Dataset of class 'exprSet'
data:geneData A subset of some expression data.
dumpPackTxt Dump Textual Description of a Package

-- E --

eList General Container for High-Throughput Assays and Experimental Metadata
esApply Apply for the Expression Data in 'exprSet'
eSet General Container for High-Throughput Assays and Experimental Metadata
eset Dataset of class 'exprSet'
exprs2excel Class for Microarray Data and Methods for Processing Them
exprSet Class for Microarray Data and Methods for Processing Them
exSet Dataset of class 'exprSet'

-- G --

geneCovariate A subset of some expression data.
geneData A subset of some expression data.
getPkgVigs List Vignette Files for a Package
golubMergeSub General Container for High-Throughput Assays and Experimental Metadata

-- L --

l2e List-Environment interactions
listLen List-Environment interactions
listOrEnv General Container for High-Throughput Assays and Experimental Metadata

-- M --

MIAME Class for Storing Microarray Experiment Information
multiassign Assign Values to a Names

-- N --

note Informational Messages

-- O --

openPDF Open PDF Files in a Standard Viewer
openVignette Open a Vignette or Show Vignette Selection Menu

-- P --

package.version Report Version of a Package
pData Class For Patient or Experiment Level Data
phenoData Class For Patient or Experiment Level Data

-- R --

read.exprSet Read Experimental Data and into an 'exprSet' Object
read.MIAME Read MIAME Information into an Instance of Class 'MIAME'
read.phenoData Read 'phenoData'
reporter Example Data Frame Object for the ReporterInfo Slot
reverseSplit A function to reverse the role of names and values in a list.
rowMax A function to compute empirical row quantiles.
rowMedians A function to compute empirical row quantiles.
rowMin A function to compute empirical row quantiles.
rowQ A function to compute empirical row quantiles.

-- S --

seD A subset of some expression data.
split Class for Microarray Data and Methods for Processing Them
strbreak Break Character Strings to Fit Width
SW General Container for High-Throughput Assays and Experimental Metadata
SWPD General Container for High-Throughput Assays and Experimental Metadata
swrep General Container for High-Throughput Assays and Experimental Metadata

-- T --

testBioCConnection A function to check internet connectivity to Bioconductor

-- U --

update2MIAME Class for Microarray Data and Methods for Processing Them

-- V --

varMetadata Class For Patient or Experiment Level Data

-- W --

write.exprs Class for Microarray Data and Methods for Processing Them