Classes for high-throughput arrays supported by oligo and crlmm


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Documentation for package ‘oligoClasses’ version 1.32.0

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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"
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
elementLengths-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