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

Functions

A Man page
A<- Man page
A<-,AlleleSet,matrix-method Man page
A<-,AlleleSet-method Man page
A,AlleleSet-method Man page
A<-,CNSet-method Man page
A,CNSet-method Man page
AffyExonPDInfo Man page
AffyExonPDInfo-class Man page
AffyExpressionPDInfo Man page
AffyExpressionPDInfo-class Man page
AffyGenePDInfo Man page
AffyGenePDInfo-class Man page
affyPlatforms Man page
AffySNPCNVPDInfo Man page
AffySNPCNVPDInfo-class Man page
AffySNPPDInfo Man page
AffySNPPDInfo-class Man page
AffySTPDInfo Man page
AffySTPDInfo-class Man page
AffyTilingPDInfo Man page
AffyTilingPDInfo-class Man page
allele Man page
allele,AlleleSet-method Man page
allele,CNSet-method Man page
AlleleSet Man page
AlleleSet-class Man page
allele,SnpFeatureSet-method Man page
annotatedDataFrameFrom,ff_matrix-method Man page
annotation,DBPDInfo-method Man page
annotation,gSetList-method Man page
annotationPackages Man page
assayDataList Man page
AssayDataList Man page
assayDataList,gSetList-method Man page
assayDataList-methods Man page
assayDataList,oligoSetList-method Man page
B Man page
B<- Man page
baf Man page
baf<- Man page
baf,BafLrrSetList-method Man page
baf,BeadStudioSetList-method Man page
baf<-,BeadStudioSet-method Man page
baf,BeadStudioSet-method Man page
BafLrrSet-class Man page
[[<-,BafLrrSetList,ANY,ANY,BafLrrSet-method Man page
[[,BafLrrSetList,ANY,ANY-method Man page
BafLrrSetList-class Man page
baf,oligoSetList-method Man page
baf<-,oligoSnpSet-method Man page
baf,oligoSnpSet-method Man page
baf,RangedSummarizedExperiment-method Man page
baf,SummarizedExperiment-method Man page
B<-,AlleleSet,matrix-method Man page
B<-,AlleleSet-method Man page
B,AlleleSet-method Man page
batch Man page
batch,CNSet-method Man page
batchNames Man page
batchNames<- Man page
batchNames<-,AssayData-method Man page
batchNames,AssayData-method Man page
batchNames<-,CNSet-method Man page
batchNames,CNSet-method Man page
batchStatistics Man page
batchStatistics<- Man page
batchStatistics<-,CNSet,AssayData-method Man page
batchStatistics,CNSet-method Man page
B<-,CNSet-method Man page
B,CNSet-method Man page
BeadStudioSet Man page
BeadStudioSet-class Man page
[[,BeadStudioSetList,ANY,ANY-method Man page
BeadStudioSetList-class Man page
bothStrands Man page
bothStrands,AlleleSet-method Man page
bothStrands,SnpFeatureSet-method Man page
calls Man page
calls<- Man page
calls<-,CNSet,matrix-method Man page
calls,CNSet-method Man page
callsConfidence<-,oligoSnpSet,matrix-method Man page
callsConfidence,oligoSnpSet-method Man page
calls,oligoSetList-method Man page
calls<-,oligoSnpSet,matrix-method Man page
calls,oligoSnpSet-method Man page
calls<-,SnpSet2,matrix-method Man page
calls,SnpSet2-method Man page
calls<-,SnpSet,matrix-method Man page
calls,SnpSet-method Man page
celfileDate Man page
celfileName Man page
checkExists Man page
checkOrder Man page
checkOrder,CopyNumberSet-method Man page
checkOrder,gSet-method Man page
checkOrder,SnpSet-method Man page
chromosome Man page
chromosome<- Man page
chromosome2integer Man page
chromosome,AnnotatedDataFrame-method Man page
chromosome<-,GenomeAnnotatedDataFrame,integer-method Man page
chromosome,GenomeAnnotatedDataFrame-method Man page
chromosome,GRangesList-method Man page
chromosome,GRanges-method Man page
chromosome<-,gSet,integer-method Man page
chromosome,gSetList-method Man page
chromosome,gSet-method Man page
chromosome-methods Man page
chromosomePositionOrder Man page
chromosome,RangedDataCNV-method Man page
chromosome,RangedDataCNV-method Man page
chromosome,RangedSummarizedExperiment-method Man page
chromosome<-,SnpSet,integer-method Man page
chromosome,SnpSet-method Man page
chromosome,SummarizedExperiment-method Man page
clone2 Man page
clone2,BafLrrSetList-method Man page
close Man page
close,AlleleSet-method Man page
close,array-method Man page
close,CNSet-method Man page
closeff Man page
closeff,CNSet-method Man page
close,matrix-method Man page
close,numeric-method Man page
cnConfidence Man page
cnConfidence<- Man page
cnConfidence<-,CopyNumberSet,matrix-method Man page
cnConfidence,CopyNumberSet-method Man page
cnConfidence<-,oligoSnpSet,matrix-method Man page
cnConfidence,oligoSnpSet-method Man page
CNSet Man page
[,CNSet,ANY-method Man page
CNSet-class Man page
[,CNSet-method Man page
coerce,AnnotatedDataFrame,GenomeAnnotatedDataFrame-method Man page
coerce,BeadStudioSet,data.frame-method Man page
coerce,CNSet,CopyNumberSet-method Man page
coerce,CNSetLM,CNSet-method Man page
coerce,CNSet,oligoSnpSet Man page
coerce,CNSet,oligoSnpSet-method Man page
coerce,gSetList,list-method Man page
coerce,oligoSnpSet,data.frame-method Man page
confs Man page
confs<- Man page
confs<-,CNSet,matrix-method Man page
confs,CNSet-method Man page
confs<-,SnpSet2,matrix-method Man page
confs,SnpSet2-method Man page
confs<-,SnpSet,matrix-method Man page
confs,SnpSet-method Man page
copyNumber Man page
copyNumber<- Man page
copyNumber<-,BeadStudioSet,ANY-method Man page
copyNumber,BeadStudioSet-method Man page
copyNumber<-,CopyNumberSet,matrix-method Man page
copyNumber,CopyNumberSet-method Man page
copyNumber,oligoSetList-method Man page
copyNumber<-,oligoSnpSet,matrix-method Man page
copyNumber,oligoSnpSet-method Man page
CopyNumberSet Man page
CopyNumberSet-class Man page
CopyNumberSet-methods Man page
corr Man page
corr,CNSet,character-method Man page
coverage2 Man page
coverage2 Man page
coverage2,GRangesList-method Man page
coverage2,GRangesList-method Man page
coverage2,GRanges-method Man page
coverage2,GRanges-method Man page
coverage2,RangedDataCNV-method Man page
createFF Man page
db Man page
db,AlleleSet-method Man page
db,DBPDInfo-method Man page
db,FeatureSet-method Man page
db,gSet-method Man page
db-methods Man page
DBPDInfo Man page
DBPDInfo-class Man page
db,SnpCnvQSet-method Man page
db,SnpQSet-method Man page
db,SnpSet-method Man page
delCluster Man page
delCluster-deprecated Man page
dims,gSetList-method Man page
efsExample Man page
elementNROWS,gSetList-method Man page
ExonFeatureSet Man page
ExonFeatureSet-class Man page
ExpressionFeatureSet Man page
ExpressionFeatureSet-class Man page
ExpressionPDInfo Man page
ExpressionPDInfo-class Man page
exprs,ExpressionSet-method Man page
exprs,FeatureSet-method Man page
exprs-methods Man page
exprs,SnpSet2-method Man page
exprs,SnpSet-method Man page
featureDataList Man page
featureDataList,gSetList-method Man page
featureDataList-methods Man page
FeatureSet Man page
FeatureSet-class Man page
featuresInRange Man page
featuresInRange,SnpSet2,RangedDataCNV-method Man page
ffdf-class Man page
ff_matrix-class Man page
ff_or_matrix-class Man page
findOverlaps,AnnotatedDataFrame,RangedDataCNV-method Man page
findOverlaps,GRanges,gSet-method Man page
findOverlaps,GRangesList,gSet-method Man page
findOverlaps,RangedDataCNV,AnnotatedDataFrame-method Man page
findOverlaps,RangedDataCNV,CNSet-method Man page
findOverlaps,RangedDataCNV,RangedDataCNV-method Man page
findOverlaps,RangedDataCNV,SnpSet-method Man page
findOverlaps,RangedDataHMM,RangedDataHMM-method Man page
flags Man page
flags,AssayData-method Man page
flags,CNSet-method Man page
GeneFeatureSet Man page
GeneFeatureSet-class Man page
GenericFeatureSet Man page
GenericFeatureSet-class Man page
GenericPDInfo Man page
GenericPDInfo-class Man page
GenomeAnnotatedDataFrame Man page
GenomeAnnotatedDataFrame-class Man page
GenomeAnnotatedDataFrameFrom Man page
GenomeAnnotatedDataFrameFrom,array-method Man page
GenomeAnnotatedDataFrameFrom,AssayData-method Man page
GenomeAnnotatedDataFrameFrom,ff_or_matrix-method Man page
GenomeAnnotatedDataFrameFrom,list-method Man page
GenomeAnnotatedDataFrameFrom,NULL-method Man page
genomeBuild Man page
genomeBuild<- Man page
genomeBuild,DBPDInfo-method Man page
genomeBuild,FeatureSet-method Man page
genomeBuild,GRanges-method Man page
genomeBuild<-,gSet,character-method Man page
genomeBuild<-,gSetList,character-method Man page
genomeBuild,gSetList-method Man page
genomeBuild,gSet-method Man page
geometry Man page
geometry,DBPDInfo-method Man page
geometry,FeatureSet-method Man page
getA Man page
getA,AlleleSet-method Man page
getArm Man page
getArm,GenomeAnnotatedDataFrame-method Man page
getArm,gSet-method Man page
getA,SnpCnvQSet-method Man page
getA,SnpQSet-method Man page
getA,TilingFeatureSet2-method Man page
getBar Man page
getCluster Man page
getCluster-deprecated Man page
getM Man page
getM,AlleleSet-method Man page
getM,SnpCnvQSet-method Man page
getM,SnpQSet-method Man page
getM,TilingFeatureSet2-method Man page
getSequenceLengths Man page
gSet Man page
gSet-class Man page
[[<-,gSetList,ANY,ANY,BafLrrSet-method Man page
[,gSetList,ANY-method Man page
gSetList-class Man page
[,gSetList-method Man page
$<-,gSetList-method Man page
$,gSetList-method Man page
i2p Man page
initialize,BeadStudioSetList-method Man page
initialize,BeadStudioSet-method Man page
initializeBigArray Man page
initializeBigMatrix Man page
initializeBigVector Man page
initialize,CNSetLM-method Man page
initialize,CNSet-method Man page
initialize,CopyNumberSet-method Man page
initialize,DBPDInfo-method Man page
initialize,eSetList-method Man page
initialize,FeatureSet-method Man page
initialize,GenomeAnnotatedDataFrame-method Man page
initialize,gSetList-method Man page
initialize,gSet-method Man page
initialize,oligoSnpSet-method Man page
initialize,SnpSet2-method Man page
initialize,SnpSuperSet-method Man page
integer2chromosome Man page
integerArray Man page
integerMatrix Man page
is.ffmatrix Man page
isPackageLoaded Man page
isSnp Man page
isSnp,character-method Man page
isSnp,GenomeAnnotatedDataFrame-method Man page
isSnp,gSet-method Man page
isSnp-methods Man page
isSnp,RangedSummarizedExperiment-method Man page
isSnp,SnpSet-method Man page
isSnp,SummarizedExperiment-method Man page
kind Man page
kind,AffyExonPDInfo-method Man page
kind,AffyExpressionPDInfo-method Man page
kind,AffyGenePDInfo-method Man page
kind,AffyHTAPDInfo-method Man page
kind,AffySNPCNVPDInfo-method Man page
kind,AffySNPPDInfo-method Man page
kind,ExpressionPDInfo-method Man page
kind,FeatureSet-method Man page
kind,GenericPDInfo-method Man page
kind,TilingPDInfo-method Man page
ldPath Man page
ldSetOptions Man page
ldStatus Man page
length,FeatureSet-method Man page
length,gSetList-method Man page
length-methods Man page
library2 Man page
list.celfiles Man page
list_or_ffdf-class Man page
lM,CNSet-method Man page
locusLevelData Man page
lrr Man page
lrr<- Man page
lrr<-,BafLrrSet,ANY-method Man page
lrr<-,BafLrrSetList,matrix-method Man page
lrr,BafLrrSetList-method Man page
lrr<-,BafLrrSet-method Man page
lrr<-,BeadStudioSet,ANY-method Man page
lrr,BeadStudioSetList-method Man page
lrr<-,BeadStudioSet-method Man page
lrr,BeadStudioSet-method Man page
lrr,RangedSummarizedExperiment-method Man page
lrr,SummarizedExperiment-method Man page
makeFeatureGRanges Man page
makeFeatureGRanges,GenomeAnnotatedDataFrame-method Man page
makeFeatureGRanges,gSetList-method Man page
makeFeatureGRanges,gSet-method Man page
manufacturer Man page
manufacturer,DBPDInfo-method Man page
manufacturer,FeatureSet-method Man page
manufacturer-methods Man page
mean,RangedDataCBS-method Man page
NgsExpressionPDInfo Man page
NgsExpressionPDInfo-class Man page
NgsTilingPDInfo Man page
NgsTilingPDInfo-class Man page
nu Man page
nu,AssayData,character-method Man page
nu,CNSet,character-method Man page
numberProbes Man page
numberProbes,GRangesList-method Man page
numberProbes,GRanges-method Man page
ocLapply Man page
ocProbesets Man page
ocSamples Man page
oligoSet Man page
oligoSetList-class Man page
oligoSnpSet-class Man page
open Man page
open,AlleleSet-method Man page
open,array-method Man page
open,CNSet-method Man page
openff Man page
openff,CNSet-method Man page
open,matrix-method Man page
open,numeric-method Man page
p2i Man page
parStatus Man page
pdPkgFromBioC Man page
phi Man page
phi,AssayData,character-method Man page
phi,CNSet,character-method Man page
platform Man page
platform,FeatureSet-method Man page
platform-methods Man page
pmFragmentLength Man page
pmFragmentLength,AffySNPPDInfo-method Man page
pmFragmentLength-methods Man page
position Man page
position<- Man page
position,AnnotatedDataFrame-method Man page
position<-,GenomeAnnotatedDataFrame,integer-method Man page
position,GenomeAnnotatedDataFrame-method Man page
position,gSetList-method Man page
position,gSet-method Man page
position-methods Man page
position<-,oligoSnpSet,integer-method Man page
position,SnpSet-method Man page
RangedDataCBS Man page
RangedDataCBS-class Man page
RangedDataCNV Man page
RangedDataCNV-class Man page
RangedDataCopyNumber-class Man page
RangedDataHMM Man page
RangedDataHMM-class Man page
requireAnnotation Man page
requireClusterPkg Man page
requireClusterPkg-deprecated Man page
requireClusterPkgSet Man page
requireClusterPkgSet-deprecated Man page
sampleNames,FeatureSet-method Man page
sampleNames,GRangesList-method Man page
sampleNames,GRanges-method Man page
sampleNames<-,gSetList,character-method Man page
sampleNames,gSetList-method Man page
sampleNames-methods Man page
sampleNames<-,RangedDataCNV,character-method Man page
sampleNames,RangedDataCNV-method Man page
scqsExample Man page
se.exprs,FeatureSet-method Man page
setCluster Man page
setCluster-deprecated Man page
setSequenceLengths Man page
sfsExample Man page
show,BeadStudioSet-method Man page
show,CNSet-method Man page
show,DBPDInfo-method Man page
show,DBPDInfo-method Man page
show,FeatureSet-method Man page
show,gSetList-method Man page
show,gSet-method Man page
sigma2,CNSet,character-method Man page
snpCallProbability,CNSet-method Man page
SnpCnvFeatureSet Man page
SnpCnvFeatureSet-class Man page
SNPCNVPDInfo Man page
SNPCNVPDInfo-class Man page
SnpFeatureSet Man page
SnpFeatureSet-class Man page
SNPPDInfo Man page
SNPPDInfo-class Man page
SnpSet2-class Man page
SnpSuperSet Man page
SnpSuperSet-class Man page
splitIndicesByLength Man page
splitIndicesByNode Man page
sqsExample Man page
state Man page
state,GRangesList-method Man page
state,GRanges-method Man page
state,RangedDataCNV-method Man page
tau2,CNSet,character-method Man page
TilingFeatureSet Man page
TilingFeatureSet2 Man page
TilingFeatureSet2-class Man page
TilingFeatureSet-class Man page
TilingPDInfo Man page
TilingPDInfo-class Man page
updateObject,BeadStudioSetList-method Man page
updateObject,BeadStudioSet-method Man page
updateObject,CNSet-method Man page
updateObject,GenomeAnnotatedDataFrame-method Man page
updateObject,oligoSnpSet-method Man page

Files

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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Please suggest features or report bugs with the GitHub issue tracker.

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