# Classes for high-throughput arrays supported by oligo and crlmm

## Documentation for package ‘oligoClasses’ version 1.49.1

- DESCRIPTION file.
- 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"
AffyExonPDInfo | Class "DBPDInfo"
AffyExonPDInfo-class | Class "DBPDInfo"
AffyExpressionPDInfo | Class "DBPDInfo"
AffyExpressionPDInfo-class | Class "DBPDInfo"
AffyGenePDInfo | Class "DBPDInfo"
AffyGenePDInfo-class | Class "DBPDInfo"
affyPlatforms | Available Affymetrix platforms for SNP arrays
AffySNPCNVPDInfo | Class "DBPDInfo"
AffySNPCNVPDInfo-class | Class "DBPDInfo"
AffySNPPDInfo | Class "DBPDInfo"
AffySNPPDInfo-class | Class "DBPDInfo"
AffySTPDInfo | Class "DBPDInfo"
AffySTPDInfo-class | Class "DBPDInfo"
AffyTilingPDInfo | Class "DBPDInfo"
AffyTilingPDInfo-class | Class "DBPDInfo"
allele | Class "AlleleSet"
allele-method | Class "AlleleSet"
allele-method | Class "CNSet"
AlleleSet | Class "AlleleSet"
AlleleSet-class | Class "AlleleSet"
annotatedDataFrameFrom-method | Class "ff_matrix"
annotation-method | Class "DBPDInfo"
annotation-method | Virtual Class for Lists of eSets
annotationPackages | Annotation Packages
AssayDataList | Create a list of assay data elements
assayDataList | Accessor for slot assayDataList in Package 'oligoClasses'
assayDataList-method | Accessor for slot assayDataList in Package 'oligoClasses'
assayDataList-method | Virtual Class for Lists of eSets
assayDataList-methods | Accessor for slot assayDataList in Package 'oligoClasses'

## -- 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
baf-method | Class '"BeadStudioSet"'
baf-method | List classes with assay data listed by chromosome
baf-method | Methods for RangedSummarizedExperiment objects
baf-method | Methods for oligoSnpSet class
baf<- | Class '"BeadStudioSet"'
baf<--method | Class '"BeadStudioSet"'
baf<--method | Methods for oligoSnpSet class
BafLrrSet-class | Class '"BeadStudioSet"'
BafLrrSetList-class | List classes with assay data listed by chromosome
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"
BeadStudioSet | Class '"BeadStudioSet"'
BeadStudioSet-class | Class '"BeadStudioSet"'
BeadStudioSetList-class | List classes with assay data listed by chromosome
bothStrands | Class "AlleleSet"
bothStrands-method | Class "AlleleSet"

## -- C --

calls | Accessors and methods for SnpSet objects
calls-method | List classes with assay data listed by chromosome
calls-method | Class "CNSet"
calls-method | Accessors and methods for SnpSet objects
calls-method | Class '"SnpSet2"'
calls-method | Methods for oligoSnpSet class
calls<- | Accessors and methods for SnpSet objects
calls<--method | Class "CNSet"
calls<--method | Accessors and methods for SnpSet objects
calls<--method | Class '"SnpSet2"'
calls<--method | Methods for oligoSnpSet class
callsConfidence-method | Methods for oligoSnpSet class
callsConfidence<--method | Methods for oligoSnpSet class
celfileDate | Cel file dates
celfileName | Extracts complete cel file name from a CNSet object
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
checkOrder-method | Container for objects with genomic annotation on SNPs
chromosome | Methods for function chromosome in package oligoClasses
chromosome-method | Methods for RangedSummarizedExperiment objects
chromosome-method | Methods for function chromosome in package oligoClasses
chromosome-method | Virtual Class for Lists of eSets
chromosome-methods | Methods for function chromosome in package oligoClasses
chromosome2integer | Converts chromosome to integer
chromosome<- | Methods for function chromosome in package oligoClasses
chromosome<--method | Methods for function chromosome in package oligoClasses
chromosomePositionOrder | Checks whether a eSet-derived class is ordered by chromosome and physical position
clone2 | List classes with assay data listed by chromosome
clone2-method | List classes with assay data listed by chromosome
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 "CNSet"
CNSet-class | Class "CNSet"
coerce,CNSet,oligoSnpSet | Class "CNSet"
coerce-method | Class '"BeadStudioSet"'
coerce-method | Class "CNSet"
coerce-method | Class '"GenomeAnnotatedDataFrame"'
coerce-method | Virtual Class for Lists of eSets
coerce-method | Methods for oligoSnpSet class
confs | Accessors and methods for SnpSet objects
confs-method | Class "CNSet"
confs-method | Accessors and methods for SnpSet objects
confs-method | Class '"SnpSet2"'
confs<- | Accessors and methods for SnpSet objects
confs<--method | Class "CNSet"
confs<--method | Accessors and methods for SnpSet objects
confs<--method | Class '"SnpSet2"'
copyNumber | Methods for class CopyNumberSet.
copyNumber-method | Class '"BeadStudioSet"'
copyNumber-method | List classes with assay data listed by chromosome
copyNumber-method | Class '"CopyNumberSet"'
copyNumber-method | Methods for oligoSnpSet class
copyNumber<- | Methods for class CopyNumberSet.
copyNumber<--method | Class '"BeadStudioSet"'
copyNumber<--method | Class '"CopyNumberSet"'
copyNumber<--method | Methods for oligoSnpSet class
CopyNumberSet | Class '"CopyNumberSet"'
CopyNumberSet-class | Class '"CopyNumberSet"'
CopyNumberSet-methods | Methods for class CopyNumberSet.
corr | Methods for class AssayData in the oligoClasses package
corr-method | Class "CNSet"
coverage2 | Methods for GRanges objects
coverage2-method | Methods for GRanges objects
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-method | Container for objects with genomic annotation on SNPs
db-methods | Get the connection to the SQLite Database
DBPDInfo | Class "DBPDInfo"
DBPDInfo-class | Class "DBPDInfo"
delCluster | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities.
delCluster-deprecated | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities.
dims-method | Virtual Class for Lists of eSets

## -- E --

efsExample | ExpressionFeatureSet Object
elementNROWS-method | Virtual Class for Lists of eSets
ExonFeatureSet | "FeatureSet" and "FeatureSet" Extensions
ExonFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions
ExpressionFeatureSet | "FeatureSet" and "FeatureSet" Extensions
ExpressionFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions
ExpressionPDInfo | Class "DBPDInfo"
ExpressionPDInfo-class | Class "DBPDInfo"
exprs-method | Class '"SnpSet2"'
exprs-method | Accessor for the 'exprs' slot
exprs-methods | Accessor for the 'exprs' slot

## -- F --

featureDataList | Accessor for slot 'featureDataList' in Package 'oligoClasses' ~~
featureDataList-method | Virtual Class for Lists of eSets
featureDataList-methods | Accessor for slot 'featureDataList' in Package 'oligoClasses' ~~
FeatureSet | "FeatureSet" and "FeatureSet" Extensions
FeatureSet-class | "FeatureSet" and "FeatureSet" Extensions
ffdf-class | Class "ffdf"
ff_matrix-class | Class "ff_matrix"
ff_or_matrix-class | Class '"ff_or_matrix"'
findOverlaps-method | Methods for GRanges objects
flags | Batch-level summary of SNP flags.
flags-method | Methods for class AssayData in the oligoClasses package
flags-method | Class "CNSet"

## -- G --

GeneFeatureSet | "FeatureSet" and "FeatureSet" Extensions
GeneFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions
GenericFeatureSet | "FeatureSet" and "FeatureSet" Extensions
GenericFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions
GenericPDInfo | Class "DBPDInfo"
GenericPDInfo-class | Class "DBPDInfo"
GenomeAnnotatedDataFrame | Class '"GenomeAnnotatedDataFrame"'
GenomeAnnotatedDataFrame-class | Class '"GenomeAnnotatedDataFrame"'
GenomeAnnotatedDataFrameFrom | Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses
GenomeAnnotatedDataFrameFrom-method | Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses
genomeBuild | Genome Build Information
genomeBuild-method | Methods for GRanges objects
genomeBuild-method | Container for objects with genomic annotation on SNPs
genomeBuild-method | Virtual Class for Lists of eSets
genomeBuild-method | Genome Build Information
genomeBuild<- | Genome Build Information
genomeBuild<--method | Container for objects with genomic annotation on SNPs
genomeBuild<--method | Virtual Class for Lists of eSets
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
getArm | Container for objects with genomic annotation on SNPs
getArm-method | Class '"GenomeAnnotatedDataFrame"'
getArm-method | Container for objects with genomic annotation on SNPs
getBar | Gets a bar of a given length.
getCluster | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities.
getCluster-deprecated | DEPRECATED FUNCTIONS. 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
getSequenceLengths | Load chromosome sequence lengths for UCSC genome build hg18 or hg19
gSet | Container for objects with genomic annotation on SNPs
gSet-class | Container for objects with genomic annotation on SNPs
gSetList-class | Virtual Class for Lists of eSets

## -- I --

i2p | Functions to convert probabilities to integers, or integers to probabilities.
initialize-method | Class '"BeadStudioSet"'
initialize-method | List classes with assay data listed by chromosome
initialize-method | Class "CNSet"
initialize-method | eSetList class
initialize-method | Class '"CopyNumberSet"'
initialize-method | Class "DBPDInfo"
initialize-method | "FeatureSet" and "FeatureSet" Extensions
initialize-method | Class '"GenomeAnnotatedDataFrame"'
initialize-method | Class '"SnpSet2"'
initialize-method | Class "SnpSuperSet"
initialize-method | Container for objects with genomic annotation on SNPs
initialize-method | Virtual Class for Lists of eSets
initialize-method | Methods for oligoSnpSet class
initializeBigArray | Initialize big matrices/vectors.
initializeBigMatrix | Initialize big matrices/vectors.
initializeBigVector | Initialize big matrices/vectors.
integer2chromosome | Converts chromosome to integer
integerArray | Coerce numeric matrix (or array) to a matrix (array) of integers, retaining dimnames.
integerMatrix | Coerce numeric matrix (or array) to a matrix (array) of integers, retaining dimnames.
is.ffmatrix | Check if object is an ff-matrix object.
isPackageLoaded | Check if package is loaded.
isSnp | Methods for Function isSnp in package oligoClasses~~
isSnp-method | Methods for RangedSummarizedExperiment objects
isSnp-method | Methods for Function isSnp in package oligoClasses~~
isSnp-methods | Methods for Function isSnp in package oligoClasses~~

## -- 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 | Virtual Class for Lists of eSets
length-method | Number of samples for FeatureSet-like objects.
length-methods | Number of samples for FeatureSet-like objects.
library2 | Supress package startup messages when loading a library
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
lrr-method | Class '"BeadStudioSet"'
lrr-method | List classes with assay data listed by chromosome
lrr-method | Methods for RangedSummarizedExperiment objects
lrr<- | Class '"BeadStudioSet"'
lrr<--method | Class '"BeadStudioSet"'
lrr<--method | List classes with assay data listed by chromosome

## -- M --

makeFeatureGRanges | Construct a GRanges object from several possible feature-level classes
makeFeatureGRanges-method | Class '"GenomeAnnotatedDataFrame"'
makeFeatureGRanges-method | Container for objects with genomic annotation on SNPs
makeFeatureGRanges-method | Virtual Class for Lists of eSets
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 "DBPDInfo"
NgsExpressionPDInfo-class | Class "DBPDInfo"
NgsTilingPDInfo | 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"
numberProbes | Methods for GRanges objects
numberProbes-method | Methods for GRanges objects

## -- 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
oligoSetList-class | List classes with assay data listed by chromosome
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

## -- 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 | Methods for function position in Package oligoClasses
position-method | Virtual Class for Lists of eSets
position-method | Methods for function position in Package oligoClasses
position-methods | Methods for function position in Package oligoClasses
position<- | Class '"GenomeAnnotatedDataFrame"'
position<--method | Class '"GenomeAnnotatedDataFrame"'
position<--method | Methods for oligoSnpSet class

## -- R --

requireAnnotation | Helper function to load packages.
requireClusterPkg | DEPRECATED FUNCTIONS. Package loaders for clusters.
requireClusterPkg-deprecated | DEPRECATED FUNCTIONS. Package loaders for clusters.
requireClusterPkgSet | DEPRECATED FUNCTIONS. Package loaders for clusters.
requireClusterPkgSet-deprecated | DEPRECATED FUNCTIONS. Package loaders for clusters.

## -- S --

sampleNames-method | Methods for GRanges objects
sampleNames-method | Virtual Class for Lists of eSets
sampleNames-method | Sample names for FeatureSet-like objects
sampleNames-methods | Sample names for FeatureSet-like objects
sampleNames<--method | Virtual Class for Lists of eSets
scqsExample | SnpCnvQSet Example
se.exprs-method | Accessor for the 'exprs' slot
setCluster | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities.
setCluster-deprecated | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities.
sfsExample | SnpFeatureSet Example
show-method | Class '"BeadStudioSet"'
show-method | Class "CNSet"
show-method | Class "DBPDInfo"
show-method | "FeatureSet" and "FeatureSet" Extensions
show-method | Container for objects with genomic annotation on SNPs
show-method | Virtual Class for Lists of eSets
sigma2-method | Class "CNSet"
snpCallProbability-method | Class "CNSet"
SnpCnvFeatureSet | "FeatureSet" and "FeatureSet" Extensions
SnpCnvFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions
SNPCNVPDInfo | Class "DBPDInfo"
SNPCNVPDInfo-class | Class "DBPDInfo"
SnpFeatureSet | "FeatureSet" and "FeatureSet" Extensions
SnpFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions
SNPPDInfo | Class "DBPDInfo"
SNPPDInfo-class | Class "DBPDInfo"
SnpSet2-class | Class '"SnpSet2"'
SnpSuperSet | Class "SnpSuperSet"
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 | Methods for GRanges objects
state-method | Methods for GRanges objects

## -- T --

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

## -- U --

updateObject-method | Class '"BeadStudioSet"'
updateObject-method | List classes with assay data listed by chromosome
updateObject-method | Class "CNSet"
updateObject-method | Class '"GenomeAnnotatedDataFrame"'
updateObject-method | Methods for oligoSnpSet class

## -- misc --

$-method | Virtual Class for Lists of eSets
$<--method | Virtual Class for Lists of eSets
[-method | Class "CNSet"
[-method | Virtual Class for Lists of eSets
[[-method | List classes with assay data listed by chromosome
[[<--method | List classes with assay data listed by chromosome
[[<--method | Virtual Class for Lists of eSets