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

Global functions
$,gSetList-method Man page
$<-,gSetList-method Man page
A Man page
A,AlleleSet-method Man page
A,CNSet-method Man page
A<- Man page
A<-,AlleleSet,matrix-method Man page
A<-,AlleleSet-method Man page
A<-,CNSet-method Man page
ADF2GDF Source code
AffyExonPDInfo Man page
AffyExonPDInfo-class Man page
AffyExpressionPDInfo Man page
AffyExpressionPDInfo-class Man page
AffyGenePDInfo Man page
AffyGenePDInfo-class 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
AlleleSet Man page
AlleleSet-class Man page
AssayDataList Man page Source code
B Man page
B,AlleleSet-method Man page
B,CNSet-method Man page
B<- Man page
B<-,AlleleSet,matrix-method Man page
B<-,AlleleSet-method Man page
B<-,CNSet-method Man page
BafLrrSet-class Man page
BafLrrSetList-class Man page
BeadStudioSet Man page
BeadStudioSet-class Man page
BeadStudioSetList-class Man page
CNSet Man page
CNSet-class Man page
CopyNumberSet Man page
CopyNumberSet-class Man page
CopyNumberSet-methods Man page
DBPDInfo Man page
DBPDInfo-class Man page
ExonFeatureSet Man page
ExonFeatureSet-class Man page
ExpressionFeatureSet Man page
ExpressionFeatureSet-class Man page
ExpressionPDInfo Man page
ExpressionPDInfo-class Man page
FeatureSet Man page
FeatureSet-class 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,AssayData-method Man page
GenomeAnnotatedDataFrameFrom,NULL-method Man page
GenomeAnnotatedDataFrameFrom,array-method Man page
GenomeAnnotatedDataFrameFrom,ff_or_matrix-method Man page
GenomeAnnotatedDataFrameFrom,list-method Man page
GenomeAnnotatedDataFrameFromArray Source code
GenomeAnnotatedDataFrameFromAssayData Source code
GenomeAnnotatedDataFrameFromList Source code
GenomeAnnotatedDataFrameFromMatrix Source code
GenomeAnnotatedDataFrameFromNULL Source code
NgsExpressionPDInfo Man page
NgsExpressionPDInfo-class Man page
NgsTilingPDInfo Man page
NgsTilingPDInfo-class Man page
RangedDataCBS Man page Source code
RangedDataCBS-class Man page
RangedDataCNV Man page Source code
RangedDataCNV-class Man page
RangedDataCopyNumber-class Man page
RangedDataHMM Man page Source code
RangedDataHMM-class Man page
SNPCNVPDInfo Man page
SNPCNVPDInfo-class Man page
SNPPDInfo Man page
SNPPDInfo-class Man page
SnpCnvFeatureSet Man page
SnpCnvFeatureSet-class Man page
SnpFeatureSet Man page
SnpFeatureSet-class Man page
SnpSet2-class Man page
SnpSuperSet Man page
SnpSuperSet-class Man page
TilingFeatureSet Man page
TilingFeatureSet-class Man page
TilingFeatureSet2 Man page
TilingFeatureSet2-class Man page
TilingPDInfo Man page
TilingPDInfo-class Man page
[,CNSet,ANY-method Man page
[,CNSet-method Man page
[,gSetList,ANY-method Man page
[,gSetList-method Man page
[[,BafLrrSetList,ANY,ANY-method Man page
[[,BeadStudioSetList,ANY,ANY-method Man page
[[<-,BafLrrSetList,ANY,ANY,BafLrrSet-method Man page
[[<-,gSetList,ANY,ANY,BafLrrSet-method Man page
addFeatureAnnotation.crlmm2 Source code
addFeatureAnnotation.pd2 Source code
affyPlatforms Man page Source code
allele Man page
allele,AlleleSet-method Man page
allele,CNSet-method 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 Source code
assayDataList Man page
assayDataList,gSetList-method Man page
assayDataList,oligoSetList-method Man page
assayDataList-methods Man page
baf Man page
baf,BafLrrSetList-method Man page
baf,BeadStudioSet-method Man page
baf,BeadStudioSetList-method Man page
baf,RangedSummarizedExperiment-method Man page
baf,SummarizedExperiment-method Man page
baf,oligoSetList-method Man page
baf,oligoSnpSet-method Man page
baf<- Man page
baf<-,BeadStudioSet-method Man page
baf<-,oligoSnpSet-method Man page
batch Man page
batch,CNSet-method Man page
batchNames Man page
batchNames,AssayData-method Man page
batchNames,CNSet-method Man page
batchNames<- Man page
batchNames<-,AssayData-method Man page
batchNames<-,CNSet-method Man page
batchStatistics Man page
batchStatistics,CNSet-method Man page
batchStatistics<- Man page
batchStatistics<-,CNSet,AssayData-method Man page
bothStrands Man page
bothStrands,AlleleSet-method Man page
bothStrands,SnpFeatureSet-method Man page
calls Man page
calls,CNSet-method Man page
calls,SnpSet-method Man page
calls,SnpSet2-method Man page
calls,oligoSetList-method Man page
calls,oligoSnpSet-method Man page
calls<- Man page
calls<-,CNSet,matrix-method Man page
calls<-,SnpSet,matrix-method Man page
calls<-,SnpSet2,matrix-method Man page
calls<-,oligoSnpSet,matrix-method Man page
callsConfidence,oligoSnpSet-method Man page
callsConfidence<-,oligoSnpSet,matrix-method Man page
celfileDate Man page Source code
celfileName Man page Source code
checkAnnotation Source code
checkExists Man page Source code
checkOrder Man page Source code
checkOrder,CopyNumberSet-method Man page
checkOrder,SnpSet-method Man page
checkOrder,gSet-method Man page
chromosome Man page
chromosome,AnnotatedDataFrame-method Man page
chromosome,GRanges-method Man page
chromosome,GRangesList-method Man page
chromosome,GenomeAnnotatedDataFrame-method Man page
chromosome,RangedDataCNV-method Man page Man page
chromosome,RangedSummarizedExperiment-method Man page
chromosome,SnpSet-method Man page
chromosome,SummarizedExperiment-method Man page
chromosome,gSet-method Man page
chromosome,gSetList-method Man page
chromosome-methods Man page
chromosome2integer Man page Source code
chromosome<- Man page
chromosome<-,GenomeAnnotatedDataFrame,integer-method Man page
chromosome<-,SnpSet,integer-method Man page
chromosome<-,gSet,integer-method Man page
chromosomePositionOrder Man page Source code
cleancdfname Source code
clone2 Man page
clone2,BafLrrSetList-method Man page
close Man page
close,AlleleSet-method Man page
close,CNSet-method Man page
close,array-method Man page
close,matrix-method Man page
close,numeric-method Man page
closeff Man page
closeff,CNSet-method Man page
cnConfidence Man page
cnConfidence,CopyNumberSet-method Man page
cnConfidence,oligoSnpSet-method Man page
cnConfidence<- Man page
cnConfidence<-,CopyNumberSet,matrix-method Man page
cnConfidence<-,oligoSnpSet,matrix-method Man page
coerce,AnnotatedDataFrame,GenomeAnnotatedDataFrame-method Man page
coerce,BeadStudioSet,data.frame-method Man page
coerce,CNSet,CopyNumberSet-method Man page
coerce,CNSet,oligoSnpSet Man page
coerce,CNSet,oligoSnpSet-method Man page
coerce,CNSetLM,CNSet-method Man page
coerce,gSetList,list-method Man page
coerce,oligoSnpSet,data.frame-method Man page
coerceToGRanges Source code
confs Man page
confs,CNSet-method Man page
confs,SnpSet-method Man page
confs,SnpSet2-method Man page
confs<- Man page
confs<-,CNSet,matrix-method Man page
confs<-,SnpSet,matrix-method Man page
confs<-,SnpSet2,matrix-method Man page
copyNumber Man page
copyNumber,BeadStudioSet-method Man page
copyNumber,CopyNumberSet-method Man page
copyNumber,oligoSetList-method Man page
copyNumber,oligoSnpSet-method Man page
copyNumber<- Man page
copyNumber<-,BeadStudioSet,ANY-method Man page
copyNumber<-,CopyNumberSet,matrix-method Man page
copyNumber<-,oligoSnpSet,matrix-method Man page
corr Man page
corr,CNSet,character-method Man page
coverage2 Man page Man page
coverage2,GRanges-method Man page Man page
coverage2,GRangesList-method Man page Man page
coverage2,RangedDataCNV-method Man page
createFF Man page Source code
db Man page
db,AlleleSet-method Man page
db,DBPDInfo-method Man page
db,FeatureSet-method Man page
db,SnpCnvQSet-method Man page
db,SnpQSet-method Man page
db,SnpSet-method Man page
db,gSet-method Man page
db-methods Man page
delCluster Man page Source code
delCluster-deprecated Man page
dims,gSetList-method Man page
duplicateBLList Source code
efsExample Man page
elementNROWS,gSetList-method Man page
exprs,ExpressionSet-method Man page
exprs,FeatureSet-method Man page
exprs,SnpSet-method Man page
exprs,SnpSet2-method Man page
exprs-methods Man page
featureDataList Man page
featureDataList,gSetList-method Man page
featureDataList-methods Man page
featuresInRange Man page
featuresInRange,SnpSet2,RangedDataCNV-method Man page
ff_matrix-class Man page
ff_or_matrix-class Man page
ffdf-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
gSet Man page
gSet-class Man page
gSetList-class Man page
genomeBuild Man page
genomeBuild,DBPDInfo-method Man page
genomeBuild,FeatureSet-method Man page
genomeBuild,GRanges-method Man page
genomeBuild,gSet-method Man page
genomeBuild,gSetList-method Man page
genomeBuild<- Man page
genomeBuild<-,gSet,character-method Man page
genomeBuild<-,gSetList,character-method Man page
geometry Man page
geometry,DBPDInfo-method Man page
geometry,FeatureSet-method Man page
getA Man page
getA,AlleleSet-method Man page
getA,SnpCnvQSet-method Man page
getA,SnpQSet-method Man page
getA,TilingFeatureSet2-method Man page
getArm Man page Source code
getArm,GenomeAnnotatedDataFrame-method Man page
getArm,gSet-method Man page
getBar Man page Source code
getCluster Man page Source code
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 Source code
i2p Man page Source code
initialize,BeadStudioSet-method Man page
initialize,BeadStudioSetList-method Man page
initialize,CNSet-method Man page
initialize,CNSetLM-method Man page
initialize,CopyNumberSet-method Man page
initialize,DBPDInfo-method Man page
initialize,FeatureSet-method Man page
initialize,GenomeAnnotatedDataFrame-method Man page
initialize,SnpSet2-method Man page
initialize,SnpSuperSet-method Man page
initialize,eSetList-method Man page
initialize,gSet-method Man page
initialize,gSetList-method Man page
initialize,oligoSnpSet-method Man page
initializeBigArray Man page Source code
initializeBigMatrix Man page Source code
initializeBigVector Man page Source code
initializeGenotypeSummaryFrom Source code
initializeLmFrom Source code
initializeLmFrom2 Source code
integer2chromosome Man page Source code
integerArray Man page Source code
integerMatrix Man page Source code
is.ffmatrix Man page Source code
isFF Source code
isPackageLoaded Man page Source code
isPdAnnotationPkg Source code
isSnp Man page
isSnp,GenomeAnnotatedDataFrame-method Man page
isSnp,RangedSummarizedExperiment-method Man page
isSnp,SnpSet-method Man page
isSnp,SummarizedExperiment-method Man page
isSnp,character-method Man page
isSnp,gSet-method Man page
isSnp-methods Man page
isSupportedAnnotation Source code
isValidGenomeAnnotatedDataFrame Source code
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
lM,CNSet-method Man page
ldPath Man page Source code
ldSetOptions Man page Source code
ldStatus Man page Source code
length,FeatureSet-method Man page
length,gSetList-method Man page
length-methods Man page
library2 Man page Source code
list.celfiles Man page Source code
list_or_ffdf-class Man page
loader Source code
locusLevelData Man page
lrr Man page
lrr,BafLrrSetList-method Man page
lrr,BeadStudioSet-method Man page
lrr,BeadStudioSetList-method Man page
lrr,RangedSummarizedExperiment-method Man page
lrr,SummarizedExperiment-method Man page
lrr<- Man page
lrr<-,BafLrrSet,ANY-method Man page
lrr<-,BafLrrSet-method Man page
lrr<-,BafLrrSetList,matrix-method Man page
lrr<-,BeadStudioSet,ANY-method Man page
lrr<-,BeadStudioSet-method Man page
makeFeatureGRanges Man page
makeFeatureGRanges,GenomeAnnotatedDataFrame-method Man page
makeFeatureGRanges,gSet-method Man page
makeFeatureGRanges,gSetList-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
nu Man page
nu,AssayData,character-method Man page
nu,CNSet,character-method Man page
numberProbes Man page
numberProbes,GRanges-method Man page
numberProbes,GRangesList-method Man page
numericMatrix Source code
ocLapply Man page Source code
ocParallelStatus Source code
ocProbesets Man page Source code
ocSamples Man page Source code
oligoSet Man page
oligoSetList-class Man page
oligoSnpSet-class Man page
onAttach Source code
open Man page
open,AlleleSet-method Man page
open,CNSet-method Man page
open,array-method Man page
open,matrix-method Man page
open,numeric-method Man page
openff Man page
openff,CNSet-method Man page
p2i Man page Source code
parStatus Man page Source code
pdPkgFromBioC Man page Source code
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,AnnotatedDataFrame-method Man page
position,GenomeAnnotatedDataFrame-method Man page
position,SnpSet-method Man page
position,gSet-method Man page
position,gSetList-method Man page
position-methods Man page
position<- Man page
position<-,GenomeAnnotatedDataFrame,integer-method Man page
position<-,oligoSnpSet,integer-method Man page
requireAnnotation Man page Source code
requireClusterPkg Man page Source code
requireClusterPkg-deprecated Man page
requireClusterPkgSet Man page Source code
requireClusterPkgSet-deprecated Man page
sampleNames,FeatureSet-method Man page
sampleNames,GRanges-method Man page
sampleNames,GRangesList-method Man page
sampleNames,RangedDataCNV-method Man page
sampleNames,gSetList-method Man page
sampleNames-methods Man page
sampleNames<-,RangedDataCNV,character-method Man page
sampleNames<-,gSetList,character-method Man page
sampleNamesGSetList Source code
scqsExample Man page
se.exprs,FeatureSet-method Man page
setCluster Man page Source code
setCluster-deprecated Man page
setSequenceLengths Man page Source code
sfsExample Man page
show,BeadStudioSet-method Man page
show,CNSet-method Man page
show,DBPDInfo-method Man page Man page
show,FeatureSet-method Man page
show,gSet-method Man page
show,gSetList-method Man page
sigma2,CNSet,character-method Man page
snpCallProbability,CNSet-method Man page
splitIndicesByLength Man page Source code
splitIndicesByNode Man page Source code
sqsExample Man page
state Man page
state,GRanges-method Man page
state,GRangesList-method Man page
state,RangedDataCNV-method Man page
tau2,CNSet,character-method Man page
updateObject,BeadStudioSet-method Man page
updateObject,BeadStudioSetList-method Man page
updateObject,CNSet-method Man page
updateObject,GenomeAnnotatedDataFrame-method Man page
updateObject,oligoSnpSet-method Man page
warningMsg Source code
oligoClasses documentation built on Nov. 17, 2017, 10:21 a.m.