oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

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This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.

Author
Benilton Carvalho and Robert Scharpf
Date of publication
None
Maintainer
Benilton Carvalho <beniltoncarvalho@gmail.com> and Robert Scharpf <rscharpf@jhsph.edu>
License
GPL (>= 2)
Version
1.36.0

View on Bioconductor

Man pages

affyPlatforms
Available Affymetrix platforms for SNP arrays
AlleleSet-class
Class "AlleleSet"
AlleleSet-methods
Compute average log-intensities / log-ratios
annotationPackages
Annotation Packages
AssayDataList
Create a list of assay data elements
assayDataList-methods
Accessor for slot assayDataList in Package 'oligoClasses'
AssayData-methods
Methods for class AssayData in the oligoClasses package
batch
The batch variable for the samples.
batchStatistics
Accessor for batch statistics uses for copy number estimation...
BeadStudioSet-class
Class '"BeadStudioSet"'
BeadStudioSetList-class
List classes with assay data listed by chromosome
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...
checkOrder
Checks whether a eSet-derived class is ordered by chromosome...
chromosome2integer
Converts chromosome to integer
chromosome-methods
Methods for function chromosome in package oligoClasses
ClassesNotExported
eSetList class
clusterOpts
Cluster and large dataset management utilities.
clusterOptsDeprecated
DEPRECATED FUNCTIONS. Cluster and large dataset management...
CNSet-class
Class "CNSet"
CopyNumberSet-class
Class '"CopyNumberSet"'
CopyNumberSet-methods
Methods for class CopyNumberSet.
createFF
Create ff objects.
data-efsExample
ExpressionFeatureSet Object
data-scqsExample
SnpCnvQSet Example
data-sfsExample
SnpFeatureSet Example
data-sqsExample
SnpQSet Example
db
Get the connection to the SQLite Database
DBPDInfo-class
Class "DBPDInfo"
defunct
oligoClasses Deprecated
exprs-methods
Accessor for the 'exprs' slot
featureDataList-methods
Accessor for slot 'featureDataList' in Package 'oligoClasses'...
FeatureSetExtensions-class
"FeatureSet" and "FeatureSet" Extensions
ffdf
Class "ffdf"
ff_matrix
Class "ff_matrix"
ff_or_matrix-class
Class '"ff_or_matrix"'
fileConnections
Open and close methods for matrices and numeric vectors
flags
Batch-level summary of SNP flags.
generics
Miscellaneous generics. Methods defined in packages that...
GenomeAnnotatedDataFrame-class
Class '"GenomeAnnotatedDataFrame"'
GenomeAnnotatedDataFrameFrom-methods
Methods for Function GenomeAnnotatedDataFrameFrom in Package...
genomeBuild
Genome Build Information
geometry-methods
Array Geometry Information
getBar
Gets a bar of a given length.
getSequenceLengths
Load chromosome sequence lengths for UCSC genome build hg18...
GRanges-methods
Methods for GRanges objects
gSet-class
Container for objects with genomic annotation on SNPs
gSetList-class
Virtual Class for Lists of eSets
i2p_p2i
Functions to convert probabilities to integers, or integers...
integerMatrix
Coerce numeric matrix (or array) to a matrix (array) of...
is.ffmatrix
Check if object is an ff-matrix object.
isPackageLoaded
Check if package is loaded.
isSnp-methods
Methods for Function isSnp in package oligoClasses~~
kind
Array type
largeObjects
Initialize big matrices/vectors.
ldOpts
Set/check large dataset options.
length-methods
Number of samples for FeatureSet-like objects.
library2
Supress package startup messages when loading a library
list.celfiles
List CEL files.
locusLevelData
Basic data elements required for the HMM
makeFeatureGRanges
Construct a GRanges object from several possible...
manufacturer-methods
Manufacturer ID for FeatureSet-like objects.
ocLapply
lapply-like function that parallelizes code when possible.
oligoSetExample
An example instance of oligoSnpSet class
oligoSnpSet-methods
Methods for oligoSnpSet class
parStatus
Checks if oligo/crlmm can use parallel resources.
pdPkgFromBioC
Get packages from BioConductor.
platform-methods
Platform Information
pmFragmentLength-methods
Information on Fragment Length
position-methods
Methods for function position in Package oligoClasses
requireAnnotation
Helper function to load packages.
requireClusterPkgSetDeprecated
DEPRECATED FUNCTIONS. Package loaders for clusters.
sampleNames-methods
Sample names for FeatureSet-like objects
SnpSet2-class
Class '"SnpSet2"'
SnpSet-methods
Accessors and methods for SnpSet objects
SnpSuperSet-class
Class "SnpSuperSet"
splitVec
Tools to distribute objects across nodes or by length.
SummarizedExperiment-methods
Methods for RangedSummarizedExperiment objects

Files in this package

oligoClasses/CHANGES
oligoClasses/DESCRIPTION
oligoClasses/NAMESPACE
oligoClasses/R
oligoClasses/R/AllClasses.R
oligoClasses/R/AllGenerics.R
oligoClasses/R/functions.R
oligoClasses/R/initialize-methods.R
oligoClasses/R/methods-AlleleSet.R
oligoClasses/R/methods-AnnotatedDataFrame.R
oligoClasses/R/methods-AssayData.R
oligoClasses/R/methods-BeadStudioSet.R
oligoClasses/R/methods-BeadStudioSetList.R
oligoClasses/R/methods-CNSet.R
oligoClasses/R/methods-CopyNumberSet.R
oligoClasses/R/methods-FeatureSet.R
oligoClasses/R/methods-GRanges.R
oligoClasses/R/methods-GenomeAnnotatedDataFrame.R
oligoClasses/R/methods-PDInfo.R
oligoClasses/R/methods-RangedDataCNV.R
oligoClasses/R/methods-SnpFeatureSet.R
oligoClasses/R/methods-SnpSet.R
oligoClasses/R/methods-SummarizedExperiment.R
oligoClasses/R/methods-gSet.R
oligoClasses/R/methods-gSetList.R
oligoClasses/R/methods-oligoSnpSet.R
oligoClasses/R/show-methods.R
oligoClasses/R/utils-general.R
oligoClasses/R/utils-lds.R
oligoClasses/R/utils-parallel.R
oligoClasses/R/zzz.R
oligoClasses/TODO
oligoClasses/data
oligoClasses/data/efsExample.rda
oligoClasses/data/locusLevelData.rda
oligoClasses/data/oligoSetExample.rda
oligoClasses/data/scqsExample.rda
oligoClasses/data/sfsExample.rda
oligoClasses/data/sqsExample.rda
oligoClasses/inst
oligoClasses/inst/NEWS.Rd
oligoClasses/inst/extdata
oligoClasses/inst/extdata/genomeAnnotatedDataFrameExample.rds
oligoClasses/inst/extdata/seqlengths_hg18.rda
oligoClasses/inst/extdata/seqlengths_hg19.rda
oligoClasses/inst/unitTests
oligoClasses/inst/unitTests/Makefile
oligoClasses/inst/unitTests/test_RangedDataCNV-class.R
oligoClasses/inst/unitTests/test_annotation.R
oligoClasses/inst/unitTests/test_classes.R
oligoClasses/inst/unitTests/test_conversions.R
oligoClasses/man
oligoClasses/man/AlleleSet-class.Rd
oligoClasses/man/AlleleSet-methods.Rd
oligoClasses/man/AssayData-methods.Rd
oligoClasses/man/AssayDataList.Rd
oligoClasses/man/BeadStudioSet-class.Rd
oligoClasses/man/BeadStudioSetList-class.Rd
oligoClasses/man/CNSet-class.Rd
oligoClasses/man/ClassesNotExported.Rd
oligoClasses/man/CopyNumberSet-class.Rd
oligoClasses/man/CopyNumberSet-methods.Rd
oligoClasses/man/DBPDInfo-class.Rd
oligoClasses/man/FeatureSetExtensions-class.Rd
oligoClasses/man/GRanges-methods.Rd
oligoClasses/man/GenomeAnnotatedDataFrame-class.Rd
oligoClasses/man/GenomeAnnotatedDataFrameFrom-methods.Rd
oligoClasses/man/SnpSet-methods.Rd
oligoClasses/man/SnpSet2-class.Rd
oligoClasses/man/SnpSuperSet-class.Rd
oligoClasses/man/SummarizedExperiment-methods.Rd
oligoClasses/man/affyPlatforms.Rd
oligoClasses/man/annotationPackages.Rd
oligoClasses/man/assayDataList-methods.Rd
oligoClasses/man/batch.Rd
oligoClasses/man/batchStatistics.Rd
oligoClasses/man/celfileDate.Rd
oligoClasses/man/celfileName.Rd
oligoClasses/man/checkExists.Rd
oligoClasses/man/checkOrder.Rd
oligoClasses/man/chromosome-methods.Rd
oligoClasses/man/chromosome2integer.Rd
oligoClasses/man/clusterOpts.Rd
oligoClasses/man/clusterOptsDeprecated.Rd
oligoClasses/man/createFF.Rd
oligoClasses/man/data-efsExample.Rd
oligoClasses/man/data-scqsExample.Rd
oligoClasses/man/data-sfsExample.Rd
oligoClasses/man/data-sqsExample.Rd
oligoClasses/man/db.Rd
oligoClasses/man/defunct.Rd
oligoClasses/man/exprs-methods.Rd
oligoClasses/man/featureDataList-methods.Rd
oligoClasses/man/ff_matrix.Rd
oligoClasses/man/ff_or_matrix-class.Rd
oligoClasses/man/ffdf.Rd
oligoClasses/man/fileConnections.Rd
oligoClasses/man/flags.Rd
oligoClasses/man/gSet-class.Rd
oligoClasses/man/gSetList-class.Rd
oligoClasses/man/generics.Rd
oligoClasses/man/genomeBuild.Rd
oligoClasses/man/geometry-methods.Rd
oligoClasses/man/getBar.Rd
oligoClasses/man/getSequenceLengths.Rd
oligoClasses/man/i2p_p2i.Rd
oligoClasses/man/integerMatrix.Rd
oligoClasses/man/is.ffmatrix.Rd
oligoClasses/man/isPackageLoaded.Rd
oligoClasses/man/isSnp-methods.Rd
oligoClasses/man/kind.Rd
oligoClasses/man/largeObjects.Rd
oligoClasses/man/ldOpts.Rd
oligoClasses/man/length-methods.Rd
oligoClasses/man/library2.Rd
oligoClasses/man/list.celfiles.Rd
oligoClasses/man/locusLevelData.Rd
oligoClasses/man/makeFeatureGRanges.Rd
oligoClasses/man/manufacturer-methods.Rd
oligoClasses/man/ocLapply.Rd
oligoClasses/man/oligoSetExample.Rd
oligoClasses/man/oligoSnpSet-methods.Rd
oligoClasses/man/parStatus.Rd
oligoClasses/man/pdPkgFromBioC.Rd
oligoClasses/man/platform-methods.Rd
oligoClasses/man/pmFragmentLength-methods.Rd
oligoClasses/man/position-methods.Rd
oligoClasses/man/requireAnnotation.Rd
oligoClasses/man/requireClusterPkgSetDeprecated.Rd
oligoClasses/man/sampleNames-methods.Rd
oligoClasses/man/splitVec.Rd
oligoClasses/tests
oligoClasses/tests/doRUnit.R
oligoClasses/vignettes
oligoClasses/vignettes/scriptsForExampleData
oligoClasses/vignettes/scriptsForExampleData/CreateExampleData.R