Classes for high-throughput arrays supported by oligo


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Documentation for package ‘oligoClasses’ version 1.10.0

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

-- A --

A Compute average log-intensities / log-ratios
A-method Compute average log-intensities / log-ratios
A<- Compute average log-intensities / log-ratios
A<--method Compute average log-intensities / log-ratios
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"
AlleleSet-class Class "AlleleSet"
annotation-method Class "DBPDInfo"
annotationPackages Annotation Packages

-- B --

B Compute average log-intensities / log-ratios
B-method Compute average log-intensities / log-ratios
B<- Compute average log-intensities / log-ratios
B<--method Compute average log-intensities / log-ratios
bothStrands Class "AlleleSet"
bothStrands-method Class "AlleleSet"

-- C --

CA Class "CNSet"
CA-method Class "CNSet"
CA<- Class "CNSet"
CA<--method Class "CNSet"
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
CB Class "CNSet"
CB-method Class "CNSet"
CB<- Class "CNSet"
CB<--method Class "CNSet"
celfileDate Cel file dates
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
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"
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.
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

-- 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 --

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.

-- 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"

-- 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

-- P --

parStatus Checks if oligo/crlmm can use parallel resources.
pdPkgFromBioC Get packages from BioConductor.
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
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 --

TilingFeatureSet-class "FeatureSet" and "FeatureSet" Extensions
TilingFeatureSet2-class "FeatureSet" and "FeatureSet" Extensions
TilingPDInfo-class Class "DBPDInfo"