Biobase: Base functions for Bioconductor


[Package List] [Top]

Documentation for package `Biobase' version 1.4.15

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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

$.eSet Class "eSet": a new exprSet class
$.exprSet Class exprSet, a class for microarray data, and methods for processing them
$.phenoData Class phenoData, a class for patient or experiment level data.

-- A --

aaMap names and characteristics of amino acids
abstract Class MIAME, a class for storing microarray experiment information
abstract,exprSet-method Class MIAME, a class for storing microarray experiment information
abstract,MIAME-method Class MIAME, a class for storing microarray experiment information
addNonExisting Add menu items to an existing/new menu of a window
addPDF2Vig Add menu items to an existing/new menu of a window
addVig2Menu Add menu items to an existing/new menu of a window
addVig4Unix Add menu items to an existing/new menu of a window
addVig4Win Add menu items to an existing/new menu of a window
addVigs2WinMenu Add menu items to an existing/new menu of a window
aggenv Class aggregator, a class of aggregators
aggenv,aggregator-method Class aggregator, a class of aggregators
aggfun Class aggregator, a class of aggregators
aggfun,aggregator-method Class aggregator, a class of aggregators
Aggregate A simple aggregation mechanism.
aggregator-class Class aggregator, a class of aggregators
annotation Class exprSet, a class for microarray data, and methods for processing them
annotation,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
annotation<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
as.data.frame.exprSet converts an exprSet to a dataframe

-- C --

characterORMIAME Class characterORMIAME, a class to make older versions compatible
characterORMIAME-class Class characterORMIAME, a class to make older versions compatible
combine Combine Data into a single object.
combine,eSet,ANY-method Class "eSet": a new exprSet class
combine,eSet,eSet-method Class "eSet": a new exprSet class
combine,phenoData,ANY-method Combine Data into a single object.
combine,phenoData,phenoData-method Combine Data into a single object.
container-class container: a class that specializes the list construct of R to provide content and access control
content container: a class that specializes the list construct of R to provide content and access control
content,container-method container: a class that specializes the list construct of R to provide content and access control
contents Function to retrieve contents of environments
contents,environment-method Function to retrieve contents of environments
copyEnv List-Environment interactions
copySubstitute Copy between connections or from an to files with configure-like name-value substitution
createPackage Create a package directory from a template, with symbol-value substitution

-- D --

description Class exprSet, a class for microarray data, and methods for processing them
description,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
description<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
dumpPackTxt dump textual description of a package

-- E --

eList Class "eSet": a new exprSet class
eList,eSet-method Class "eSet": a new exprSet class
eList<-,eSet,environment-method Class "eSet": a new exprSet class
eList<-,eSet,exprList-method Class "exprList" a class union of a list and an environment.
eList<-,eSet,list-method Class "eSet": a new exprSet class
esApply Apply for the expression data in an exprSet
eset A dataset of class exprSet
eSet-class Class "eSet": a new exprSet class
expinfo Class MIAME, a class for storing microarray experiment information
expinfo,MIAME-method Class MIAME, a class for storing microarray experiment information
exprList-class Class "exprList" a class union of a list and an environment.
exprMatrix-class Class union for objects behaving like a matrix
exprs Class exprSet, a class for microarray data, and methods for processing them
exprs,eSet-method Class "eSet": a new exprSet class
exprs,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
exprs2excel Class exprSet, a class for microarray data, and methods for processing them
exprs2excel,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
exprs<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
exprSet Class exprSet, a class for microarray data, and methods for processing them
exprSet-class Class exprSet, a class for microarray data, and methods for processing them

-- G --

geneCov A subset of some expression data.
geneData A subset of some expression data.
geneNames Class exprSet, a class for microarray data, and methods for processing them
geneNames,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
geneNames<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
getExpData Class "eSet": a new exprSet class
getExpData,eSet,character-method Class "eSet": a new exprSet class
getPkgVigs A function to list PDF files for a package

-- H --

hybridizations Class MIAME, a class for storing microarray experiment information
hybridizations,MIAME-method Class MIAME, a class for storing microarray experiment information

-- I --

initfun Class aggregator, a class of aggregators
initfun,aggregator-method Class aggregator, a class of aggregators
iter Methods for the generic iter.
iter,exprSet,character,function-method Methods for the generic iter.
iter,exprSet,missing,function-method Methods for the generic iter.
iter,exprSet,missing,list-method Methods for the generic iter.
iter-methods Methods for the generic iter.

-- L --

l2e List-Environment interactions
length,container-method container: a class that specializes the list construct of R to provide content and access control
listLen List-Environment interactions
locked container: a class that specializes the list construct of R to provide content and access control
locked,container-method container: a class that specializes the list construct of R to provide content and access control

-- M --

MIAME Class MIAME, a class for storing microarray experiment information
MIAME-class Class MIAME, a class for storing microarray experiment information
multiassign Assign Values to a Names
multiget Return a list containing the Values of the supplied variables.

-- N --

normControls Class MIAME, a class for storing microarray experiment information
normControls,MIAME-method Class MIAME, a class for storing microarray experiment information
notes Class exprSet, a class for microarray data, and methods for processing them
notes,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
notes<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them

-- O --

openPDF A function to view PDF files
openVignette Open a selected Vignette
otherInfo Class MIAME, a class for storing microarray experiment information
otherInfo,MIAME-method Class MIAME, a class for storing microarray experiment information

-- P --

package.version A function to report package versions
pData Class exprSet, a class for microarray data, and methods for processing them
pData,eSet-method Class "eSet": a new exprSet class
pData,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
pData,phenoData-method Class phenoData, a class for patient or experiment level data.
pData<-,eSet-method Class "eSet": a new exprSet class
pData<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
pData<-,phenoData-method Class phenoData, a class for patient or experiment level data.
phenoData Class exprSet, a class for microarray data, and methods for processing them
phenoData,eSet-method Class "eSet": a new exprSet class
phenoData,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
phenoData-class Class phenoData, a class for patient or experiment level data.
phenoData<-,eSet,phenoData-method Class "eSet": a new exprSet class
phenoData<-,exprSet,phenoData-method Class exprSet, a class for microarray data, and methods for processing them
phenoData<-,pheno Class phenoData, a class for patient or experiment level data.
preproc Class MIAME, a class for storing microarray experiment information
preproc,MIAME-method Class MIAME, a class for storing microarray experiment information

-- R --

read.exprSet A function to read experimental data and create an exprSet object using the data read in as a text file
read.MIAME Read MIAME information
read.phenoData Read phenoData

-- S --

sampleNames Class exprSet, a class for microarray data, and methods for processing them
sampleNames,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
sampleNames<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
samples Class MIAME, a class for storing microarray experiment information
samples,MIAME-method Class MIAME, a class for storing microarray experiment information
se.exprs Class exprSet, a class for microarray data, and methods for processing them
se.exprs,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
se.exprs<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
show,container-method container: a class that specializes the list construct of R to provide content and access control
show,eSet-method Class "eSet": a new exprSet class
show,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
show,MIAME-method Class MIAME, a class for storing microarray experiment information
show,phenoData-method Class phenoData, a class for patient or experiment level data.
split,exprSet,vector-method Class exprSet, a class for microarray data, and methods for processing them
split,phenoData,vector-method Class phenoData, a class for patient or experiment level data.

-- T --

testBioCConnection A function to check internet connectivity to Bioconductor

-- U --

update2MIAME Class exprSet, a class for microarray data, and methods for processing them
update2MIAME,exprSet-method Class exprSet, a class for microarray data, and methods for processing them

-- V --

varLabels Class exprSet, a class for microarray data, and methods for processing them
varLabels,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
varLabels,phenoData-method Class phenoData, a class for patient or experiment level data.

-- W --

write.exprs Class exprSet, a class for microarray data, and methods for processing them
write.exprs,exprSet-method Class exprSet, a class for microarray data, and methods for processing them

-- misc --

[,container-method container: a class that specializes the list construct of R to provide content and access control
[,eSet-method Class "eSet": a new exprSet class
[,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
[,phenoData-method Class phenoData, a class for patient or experiment level data.
[[,container-method container: a class that specializes the list construct of R to provide content and access control
[[,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
[[,phenoData-method Class phenoData, a class for patient or experiment level data.
[[<-,container-method container: a class that specializes the list construct of R to provide content and access control
[[<-,exprSet-method Class exprSet, a class for microarray data, and methods for processing them
[[<-,phenoData-method Class phenoData, a class for patient or experiment level data.