Classes for high-throughput arrays supported by oligo and crlmm

Documentation for package ‘oligoClasses’ version 1.16.0

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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"
baf	Miscellaneous generics. Methods defined in packages that depend on oligoClasses
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 and methods for SnpSet objects
calls-method	Accessors and methods for SnpSet objects
calls-method	Methods for oligoSnpSet class
calls<-	Accessors and methods for SnpSet objects
calls<--method	Accessors and methods for SnpSet objects
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.
checkOrder	Checks whether a eSet-derived class is ordered by chromosome and physical position
checkOrder-method	Class '"CopyNumberSet"'
checkOrder-method	Accessors and methods for SnpSet objects
chromosome	Accessors for eSet extensions
chromosome-method	Classes in MinimumDistance for data on ranges
chromosome-method	Accessors for eSet extensions
chromosome2integer	Converts chromosome to integer
chromosome<-	Accessors for eSet extensions
chromosome<--method	Accessors for eSet extensions
close	Open and close methods for matrices and numeric vectors
close-method	Compute average log-intensities / log-ratios
close-method	Class "CNSet"
close-method	Open and close methods for matrices and numeric vectors
closeff	Open and close methods for matrices and numeric vectors
closeff-method	Open and close methods for matrices and numeric vectors
cnConfidence	Methods for class CopyNumberSet.
cnConfidence-method	Class '"CopyNumberSet"'
cnConfidence-method	Methods for oligoSnpSet class
cnConfidence<-	Methods for class CopyNumberSet.
cnConfidence<--method	Class '"CopyNumberSet"'
cnConfidence<--method	Methods for oligoSnpSet class
CNSet-class	Class "CNSet"
coerce,CNSet,oligoSnpSet	Class "CNSet"
coerce-method	Class "CNSet"
coerce-method	Utility functions for RangedData extensions for storing ranged data on copy number variants.
coerce-method	Methods for oligoSnpSet class
confs	Accessors and methods for SnpSet objects
confs-method	Accessors and methods for SnpSet objects
confs<-	Accessors and methods for SnpSet objects
confs<--method	Accessors and methods for SnpSet objects
copyNumber	Methods for class CopyNumberSet.
copyNumber-method	Class '"CopyNumberSet"'
copyNumber-method	Methods for oligoSnpSet class
copyNumber<-	Methods for class CopyNumberSet.
copyNumber<--method	Class '"CopyNumberSet"'
copyNumber<--method	Methods for oligoSnpSet class
CopyNumberSet-class	Class '"CopyNumberSet"'
CopyNumberSet-methods	Methods for class CopyNumberSet.
corr	Methods for class AssayData in the oligoClasses package
corr-method	Class "CNSet"
coverage2	Utility functions for RangedData extensions for storing ranged data on copy number variants.
coverage2-method	Classes in MinimumDistance for data on ranges
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
featuresInRange	Find feature index in a genomic interval
featuresInRange-method	Classes in MinimumDistance for data on ranges
ffdf-class	Class "ffdf"
ff_matrix-class	Class "ff_matrix"
findOverlaps	Find markers that overlap with a query set of ranges
findOverlaps-method	Find markers that overlap with a query set of ranges
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	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"
locusLevelData	Basic data elements required for the HMM
lrr	Miscellaneous generics. Methods defined in packages that depend on oligoClasses

-- 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.
oligoSet	An example instance of oligoSnpSet class
oligoSnpSet-class	Methods for oligoSnpSet class
open	Open and close methods for matrices and numeric vectors
open-method	Compute average log-intensities / log-ratios
open-method	Class "CNSet"
open-method	Open and close methods for matrices and numeric vectors
openff	Open and close methods for matrices and numeric vectors
openff-method	Open and close methods for matrices and numeric vectors
order	Methods for CopyNumberSet objects
order-method	Methods for CopyNumberSet objects

-- 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	Accessors for eSet extensions
position-method	Accessors for eSet extensions

-- R --

RangedDataCBS	Utility functions for RangedData extensions for storing ranged data on copy number variants.
RangedDataCBS-class	Classes in MinimumDistance for data on ranges
RangedDataCNV	Utility functions for RangedData extensions for storing ranged data on copy number variants.
RangedDataCNV-class	Classes in MinimumDistance for data on ranges
RangedDataCopyNumber-class	Classes in MinimumDistance for data on ranges
RangedDataHMM	Utility functions for RangedData extensions for storing ranged data on copy number variants.
RangedDataHMM-class	Classes in MinimumDistance for data on ranges
requireAnnotation	Helper function to load packages.
requireClusterPkg	Package loaders for clusters.
requireClusterPkgSet	Package loaders for clusters.

-- S --

sampleNames-method	Classes in MinimumDistance for data on ranges
sampleNames-method	Sample names for FeatureSet-like objects
sampleNames-methods	Sample names for FeatureSet-like objects
sampleNames<--method	Utility functions for RangedData extensions for storing ranged data on copy number variants.
scqsExample	SnpCnvQSet Example
se.exprs-method	Accessor for the 'exprs' slot
setCluster	Cluster and large dataset management utilities.
sfsExample	SnpFeatureSet Example
show-method	Class "CNSet"
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
state	Utility functions for RangedData extensions for storing ranged data on copy number variants.
state-method	Classes in MinimumDistance for data on ranges

-- T --

tau2-method	Class "CNSet"
TilingFeatureSet-class	"FeatureSet" and "FeatureSet" Extensions
TilingFeatureSet2-class	"FeatureSet" and "FeatureSet" Extensions
TilingPDInfo-class	Class "DBPDInfo"
todf-method	Classes in MinimumDistance for data on ranges

-- U --

updateObject-method

Class "CNSet"

-- misc --

[-method

Class "CNSet"