benilton/oligoClasses-release
Classes for high-throughput arrays supported by oligo and crlmm

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450
Source code
33
Man pages
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benilton/oligoClasses-release: Classes for high-throughput arrays supported by oligo and crlmm
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API

API for benilton/oligoClasses-release
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
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
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
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
NgsExpressionPDInfo Man page
NgsExpressionPDInfo-class Man page
NgsTilingPDInfo Man page
NgsTilingPDInfo-class 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
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
affyPlatforms Man page
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
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,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
celfileName Man page
checkExists Man page
checkOrder Man page
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,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
chromosome<- Man page
chromosome<-,GenomeAnnotatedDataFrame,integer-method Man page
chromosome<-,SnpSet,integer-method Man page
chromosome<-,gSet,integer-method Man page
chromosomePositionOrder Man page
clone Man page
clone,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
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
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
delCluster-deprecated Man page
dims,gSetList-method Man page
efsExample Man page
elementLengths,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
getArm,GenomeAnnotatedDataFrame-method Man page
getArm,gSet-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
i2p Man page
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
initializeBigMatrix Man page
initializeBigVector Man page
integer2chromosome Man page
integerArray Man page
integerMatrix Man page
is.ffmatrix Man page
isPackageLoaded Man page
isSnp Man page
isSnp,GenomeAnnotatedDataFrame-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
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,TilingPDInfo-method Man page
lM,CNSet-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
locusLevelData Man page
lrr Man page
lrr,BafLrrSetList-method Man page
lrr,BeadStudioSet-method Man page
lrr,BeadStudioSetList-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
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,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
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,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
requireClusterPkg Man page
requireClusterPkg-deprecated Man page
requireClusterPkgSet Man page
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
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 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
splitIndicesByNode Man page
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
benilton/oligoClasses-release documentation built on May 12, 2019, 11:51 a.m.

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