Classes for high-throughput arrays supported by oligo and crlmm


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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"