Oligonucleotide Arrays


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Documentation for package `oligo' version 0.99.15

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A B C E F G H I L M N P R S T X

$.platformDesign Class "platformDesign"
$.platformDesign, FeatureSet-method Class "FeatureSet"

-- A --

allele Retrieve allele from PDEnv for SNP arrays
allele,FeatureSet-method Class "FeatureSet"
as.data.frame.platformDesign Coerce to a Data Frame

-- B --

basecontent Boxplot
bg.correct.rma Background Correction
boxplot,FeatureSet-method Class "FeatureSet"

-- C --

characterOrNULL-class Class "characterOrNULL"
cleanPlatformName Naming PDEnvs

-- E --

ExpressionFeatureSet-class Subclasses of FeatureSet.
exprs, FeatureSet-method Class "FeatureSet"
exprs,FeatureSet-method Methods for FeatureSet objects

-- F --

featureIndex Indexes of features on the array
featureIndex,FeatureSet-method Class "FeatureSet"
featureInfo Platform Design Environment
FeatureSet-class Class "FeatureSet"

-- G --

geneNames,FeatureSet-method Class "FeatureSet"
getPD Platform Design accessor
getPlatformDesign Platform Design accessor
getPlatformDesign,FeatureSet-method Class "FeatureSet"

-- H --

hist,FeatureSet-method Class "FeatureSet"

-- I --

i2xy Index <-> XY
image,FeatureSet-method Class "FeatureSet"
indexFeatureSetName Indexes for feature sets.
indexFeatureSetName,FeatureSet-method Class "FeatureSet"
initialize, FeatureSet-method Methods for FeatureSet objects
initialize,AnnotatedDataFrame-method Methods for Class Initialization
initialize,ANY-method Methods for Class Initialization
initialize,environment-method Methods for Class Initialization
initialize,eSet-method Methods for Class Initialization
initialize,ExpressionSet-method Methods for Class Initialization
initialize,FeatureSet-method Methods for Class Initialization
initialize,signature-method Methods for Class Initialization
initialize,SnpSet-method Methods for Class Initialization
initialize,traceable-method Methods for Class Initialization
initialize-methods Methods for Class Initialization

-- L --

length,FeatureSet-method Class "FeatureSet"
list.celfiles Functions to list CEL and XYS files.
list.xysfiles Functions to list CEL and XYS files.

-- M --

manufacturer Accessors for FeatureSet objects.
manufacturer, FeatureSet-method Class "FeatureSet"
manufacturer,FeatureSet-method Methods for FeatureSet objects
manufacturer<-, FeatureSet-method Class "FeatureSet"
manufacturer<-,FeatureSet-method Methods for FeatureSet objects
mm Accessors for perfect match (pm) and mismatch (mm) probes.
mm,FeatureSet-method Class "FeatureSet"
mm<-,FeatureSet-method Class "FeatureSet"
mmindex Accessors for perfect match (pm) and mismatch (mm) probes.
mmindex,FeatureSet-method Class "FeatureSet"
mmindex,platformDesign-method Class "platformDesign"
mmSequence Methods to deal with sequences.

-- N --

names Platform Design variables
names,platformDesign-method Class "platformDesign"
ncol,FeatureSet-method Class "FeatureSet"
normalize.FeatureSet.quantiles Quantile Normalization Functions
normalize.quantiles Quantile Normalization Functions
npixels Accessors for FeatureSet objects.
npixels,FeatureSet-method Class "FeatureSet"
nProbes Number of probes on the array
nProbes,platformDesign-method Class "platformDesign"
nrow Accessors for the dimensions of the array
nrow,FeatureSet-method Class "FeatureSet"

-- P --

platform Accessors for FeatureSet objects.
platform,FeatureSet-method Class "FeatureSet"
platform<-, FeatureSet-method Class "FeatureSet"
platform<-,FeatureSet-method Methods for FeatureSet objects
platformDesign-class Class "platformDesign"
platformDesignName The platform design object name.
platformDesignName,FeatureSet-method Class "FeatureSet"
plotDensity Plot Densities
pm Accessors for perfect match (pm) and mismatch (mm) probes.
pm,FeatureSet-method Class "FeatureSet"
pm<-,FeatureSet-method Class "FeatureSet"
pmindex Accessors for perfect match (pm) and mismatch (mm) probes.
pmindex,FeatureSet-method Class "FeatureSet"
pmindex,platformDesign-method Class "platformDesign"
pmSequence Methods to deal with sequences.
probeNames Feature Set Names
probeNames, FeatureSet-method Methods for FeatureSet objects
probeNames,FeatureSet,characterOrNULL-method Probe Names
probeNames,FeatureSet-method Class "FeatureSet"
probeNames,platformDesign,characterOrNULL-method Probe Names
probeNames,platformDesign-method Class "platformDesign"
probeNames-methods Probe Names

-- R --

read.affybatch Affymetrix CEL files parser
read.celfiles Affymetrix CEL files parser
read.xysfiles XYS files parser.
readonexysfile XYS files parser.
readxysHeader XYS files parser.
rma Robust multi-array average

-- S --

sd,FeatureSet-method Class "FeatureSet"
sequenceDesignMatrix Methods to deal with sequences.
show,FeatureSet-method Class "FeatureSet"
show,platformDesign-method Class "platformDesign"
SnpFeatureSet-class Subclasses of FeatureSet.
stuffForXYSandCELreaders Affymetrix CEL files parser

-- T --

TilingFeatureSet-class Subclasses of FeatureSet.
type Accessors for FeatureSet objects.

-- X --

xy2i Index <-> XY