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

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

AuthorBenilton Carvalho and Robert Scharpf
Date of publicationNone
MaintainerBenilton Carvalho <beniltoncarvalho@gmail.com> and Robert Scharpf <rscharpf@jhsph.edu>
LicenseGPL (>= 2)
Version1.36.0

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

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