Classes for high-throughput arrays supported by oligo

Documentation for package ‘oligoClasses’ version 1.12.2

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.
Package NEWS.

Help Pages

A B C D E F G I K L M N O P R S T U misc

-- A --

A	Compute average log-intensities / log-ratios
A-method	Compute average log-intensities / log-ratios
A-method	Class "CNSet"
A<-	Compute average log-intensities / log-ratios
A<--method	Compute average log-intensities / log-ratios
A<--method	Class "CNSet"
addFeatureAnnotation	Add genomic annotation (chromosome, position) for several SNP platforms.
AffyExonPDInfo-class	Class "DBPDInfo"
AffyExpressionPDInfo-class	Class "DBPDInfo"
AffyGenePDInfo-class	Class "DBPDInfo"
affyPlatforms	Available Affymetrix platforms for SNP arrays
AffySNPCNVPDInfo-class	Class "DBPDInfo"
AffySNPPDInfo-class	Class "DBPDInfo"
AffySTPDInfo-class	Class "DBPDInfo"
AffyTilingPDInfo-class	Class "DBPDInfo"
allele	Class "AlleleSet"
allele-method	Class "AlleleSet"
allele-method	Class "CNSet"
AlleleSet-class	Class "AlleleSet"
annotatedDataFrameFrom-method	Class "ff_matrix"
annotation-method	Class "DBPDInfo"
annotationPackages	Annotation Packages

-- B --

B	Compute average log-intensities / log-ratios
B-method	Compute average log-intensities / log-ratios
B-method	Class "CNSet"
B<-	Compute average log-intensities / log-ratios
B<--method	Compute average log-intensities / log-ratios
B<--method	Class "CNSet"
batch	The batch variable for the samples.
batch-method	Class "CNSet"
batchNames	The batch variable for the samples.
batchNames-method	Methods for class AssayData in the oligoClasses package
batchNames-method	Class "CNSet"
batchNames<-	The batch variable for the samples.
batchNames<--method	Methods for class AssayData in the oligoClasses package
batchNames<--method	Class "CNSet"
batchStatistics	Accessor for batch statistics uses for copy number estimation and storage of model parameters
batchStatistics-method	Class "CNSet"
batchStatistics<-	Accessor for batch statistics uses for copy number estimation and storage of model parameters
batchStatistics<--method	Class "CNSet"
bothStrands	Class "AlleleSet"
bothStrands-method	Class "AlleleSet"

-- C --

calls	Accessors for Calls and Confidences on a SnpSet object
calls-method	Accessors for Calls and Confidences on a SnpSet object
calls-method	Methods for oligoSnpSet class
calls<-	Accessors for Calls and Confidences on a SnpSet object
calls<--method	Accessors for Calls and Confidences on a SnpSet object
calls<--method	Methods for oligoSnpSet class
callsConfidence-method	Methods for oligoSnpSet class
callsConfidence<--method	Methods for oligoSnpSet class
celfileDate	Cel file dates
checkExists	Checks to see whether an object exists and, if not, executes the appropriate function.
chromosome	Accessors for eSet extensions
chromosome-method	Accessors for eSet extensions
chromosome2integer	Converts chromosome to integer
chromosome<-	Accessors for eSet extensions
chromosome<--method	Accessors for eSet extensions
close	Compute average log-intensities / log-ratios
close-method	Compute average log-intensities / log-ratios
close-method	Class "CNSet"
cnConfidence	Methods for class CopyNumberSet.
cnConfidence-method	Methods for class CopyNumberSet.
cnConfidence-method	Methods for oligoSnpSet class
cnConfidence<-	Methods for class CopyNumberSet.
cnConfidence<--method	Methods for class CopyNumberSet.
cnConfidence<--method	Methods for oligoSnpSet class
CNSet-class	Class "CNSet"
coerce,CNSet,oligoSnpSet	Class "CNSet"
coerce-method	Class "CNSet"
confs	Accessors for Calls and Confidences on a SnpSet object
confs-method	Accessors for Calls and Confidences on a SnpSet object
confs<-	Accessors for Calls and Confidences on a SnpSet object
confs<--method	Accessors for Calls and Confidences on a SnpSet object
copyNumber	Methods for class CopyNumberSet.
copyNumber-method	Methods for class CopyNumberSet.
copyNumber-method	Methods for oligoSnpSet class
copyNumber<-	Methods for class CopyNumberSet.
copyNumber<--method	Methods for class CopyNumberSet.
copyNumber<--method	Methods for oligoSnpSet class
CopyNumberSet-methods	Methods for class CopyNumberSet.
corr	Methods for class AssayData in the oligoClasses package
corr-method	Class "CNSet"
createFF	Create ff objects.

-- D --

db	Get the connection to the SQLite Database
db-method	Class "AlleleSet"
db-method	Get the connection to the SQLite Database
db-methods	Get the connection to the SQLite Database
DBPDInfo-class	Class "DBPDInfo"
delCluster	Cluster and large dataset management utilities.

-- E --

efsExample	ExpressionFeatureSet Object
ExonFeatureSet-class	"FeatureSet" and "FeatureSet" Extensions
ExpressionFeatureSet-class	"FeatureSet" and "FeatureSet" Extensions
ExpressionPDInfo-class	Class "DBPDInfo"
exprs-method	Accessor for the 'exprs' slot
exprs-methods	Accessor for the 'exprs' slot

-- F --

FeatureSet-class	"FeatureSet" and "FeatureSet" Extensions
ffdf-class	Class "ffdf"
ff_matrix-class	Class "ff_matrix"
flags	Batch-level summary of SNP flags.
flags-method	Methods for class AssayData in the oligoClasses package
flags-method	Class "CNSet"

-- G --

GeneFeatureSet-class	"FeatureSet" and "FeatureSet" Extensions
genomeBuild	Genome Build Information
genomeBuild-method	Genome Build Information
geometry	Array Geometry Information
geometry-method	Array Geometry Information
getA	Compute average log-intensities / log-ratios
getA-method	Class "AlleleSet"
getA-method	Compute average log-intensities / log-ratios
getBar	Gets a bar of a given length.
getCluster	Cluster and large dataset management utilities.
getM	Compute average log-intensities / log-ratios
getM-method	Class "AlleleSet"
getM-method	Compute average log-intensities / log-ratios

-- I --

i2p	Functions to convert probabilities to integers, or integers to probabilities.
initialize-method	Class "CNSet"
initialize-method	Methods for class CopyNumberSet.
initialize-method	Class "DBPDInfo"
initialize-method	"FeatureSet" and "FeatureSet" Extensions
initialize-method	Class "SnpSuperSet"
initialize-method	Methods for oligoSnpSet class
initializeBigMatrix	Initialize big matrices/vectors.
initializeBigVector	Initialize big matrices/vectors.
is.ffmatrix	Check if object is an ff-matrix object.
isPackageLoaded	Check if package is loaded.
isSnp	Accessors for eSet extensions
isSnp-method	Accessors for eSet extensions

-- K --

kind	Array type
kind-method	Array type

-- L --

ldPath	Set/check large dataset options.
ldSetOptions	Set/check large dataset options.
ldStatus	Set/check large dataset options.
length-method	Number of samples for FeatureSet-like objects.
length-methods	Number of samples for FeatureSet-like objects.
list.celfiles	List CEL files.
list_or_ffdf-class	Class "ffdf"

-- M --

manufacturer	Manufacturer ID for FeatureSet-like objects.
manufacturer-method	Manufacturer ID for FeatureSet-like objects.
manufacturer-methods	Manufacturer ID for FeatureSet-like objects.

-- N --

NgsExpressionPDInfo-class	Class "DBPDInfo"
NgsTilingPDInfo-class	Class "DBPDInfo"
nu	Methods for class AssayData in the oligoClasses package
nu-method	Methods for class AssayData in the oligoClasses package
nu-method	Class "CNSet"

-- O --

ocLapply	lapply-like function that parallelizes code when possible.
ocProbesets	Cluster and large dataset management utilities.
ocSamples	Cluster and large dataset management utilities.
oligoSnpSet-class	Methods for oligoSnpSet class
open	Compute average log-intensities / log-ratios
open-method	Compute average log-intensities / log-ratios
open-method	Class "CNSet"

-- P --

p2i	Functions to convert probabilities to integers, or integers to probabilities.
parStatus	Checks if oligo/crlmm can use parallel resources.
pdPkgFromBioC	Get packages from BioConductor.
phi	Methods for class AssayData in the oligoClasses package
phi-method	Methods for class AssayData in the oligoClasses package
phi-method	Class "CNSet"
platform	Platform Information
platform-method	Platform Information
platform-methods	Platform Information
pmFragmentLength	Information on Fragment Length
pmFragmentLength-method	Information on Fragment Length
pmFragmentLength-methods	Information on Fragment Length
position	Accessor to position information
position-method	Accessors for eSet extensions

-- R --

requireAnnotation	Helper function to load packages.
requireClusterPkg	Package loaders for clusters.
requireClusterPkgSet	Package loaders for clusters.

-- S --

sampleNames-method	Sample names for FeatureSet-like objects
sampleNames-methods	Sample names for FeatureSet-like objects
scqsExample	SnpCnvQSet Example
se.exprs-method	Accessor for the 'exprs' slot
setCluster	Cluster and large dataset management utilities.
sfsExample	SnpFeatureSet Example
show-method	Class "DBPDInfo"
show-method	"FeatureSet" and "FeatureSet" Extensions
sigma2-method	Class "CNSet"
SnpCnvFeatureSet-class	"FeatureSet" and "FeatureSet" Extensions
SNPCNVPDInfo-class	Class "DBPDInfo"
SnpFeatureSet-class	"FeatureSet" and "FeatureSet" Extensions
SNPPDInfo-class	Class "DBPDInfo"
SnpSuperSet-class	Class "SnpSuperSet"
splitIndicesByLength	Tools to distribute objects across nodes or by length.
splitIndicesByNode	Tools to distribute objects across nodes or by length.
sqsExample	SnpQSet Example

-- T --

tau2-method	Class "CNSet"
TilingFeatureSet-class	"FeatureSet" and "FeatureSet" Extensions
TilingFeatureSet2-class	"FeatureSet" and "FeatureSet" Extensions
TilingPDInfo-class	Class "DBPDInfo"

-- U --

updateObject-method

Class "CNSet"

-- misc --

[-method

Class "CNSet"