A B C D E F G I K L M N O P R S T U misc
A | Compute average log-intensities / log-ratios |
A-method | Compute average log-intensities / log-ratios |
A-method | Class "CNSet" |
A<- | Compute average log-intensities / log-ratios |
A<--method | Compute average log-intensities / log-ratios |
A<--method | Class "CNSet" |
AffyExonPDInfo | Class "DBPDInfo" |
AffyExonPDInfo-class | Class "DBPDInfo" |
AffyExpressionPDInfo | Class "DBPDInfo" |
AffyExpressionPDInfo-class | Class "DBPDInfo" |
AffyGenePDInfo | Class "DBPDInfo" |
AffyGenePDInfo-class | Class "DBPDInfo" |
affyPlatforms | Available Affymetrix platforms for SNP arrays |
AffySNPCNVPDInfo | Class "DBPDInfo" |
AffySNPCNVPDInfo-class | Class "DBPDInfo" |
AffySNPPDInfo | Class "DBPDInfo" |
AffySNPPDInfo-class | Class "DBPDInfo" |
AffySTPDInfo | Class "DBPDInfo" |
AffySTPDInfo-class | Class "DBPDInfo" |
AffyTilingPDInfo | Class "DBPDInfo" |
AffyTilingPDInfo-class | Class "DBPDInfo" |
allele | Class "AlleleSet" |
allele-method | Class "AlleleSet" |
allele-method | Class "CNSet" |
AlleleSet | Class "AlleleSet" |
AlleleSet-class | Class "AlleleSet" |
annotatedDataFrameFrom-method | Class "ff_matrix" |
annotation-method | Class "DBPDInfo" |
annotation-method | Virtual Class for Lists of eSets |
annotationPackages | Annotation Packages |
AssayDataList | Create a list of assay data elements |
assayDataList | Accessor for slot assayDataList in Package 'oligoClasses' |
assayDataList-method | Accessor for slot assayDataList in Package 'oligoClasses' |
assayDataList-method | Virtual Class for Lists of eSets |
assayDataList-methods | Accessor for slot assayDataList in Package 'oligoClasses' |
B | Compute average log-intensities / log-ratios |
B-method | Compute average log-intensities / log-ratios |
B-method | Class "CNSet" |
B<- | Compute average log-intensities / log-ratios |
B<--method | Compute average log-intensities / log-ratios |
B<--method | Class "CNSet" |
baf | Miscellaneous generics. Methods defined in packages that depend on oligoClasses |
baf-method | Class '"BeadStudioSet"' |
baf-method | List classes with assay data listed by chromosome |
baf-method | Methods for RangedSummarizedExperiment objects |
baf-method | Methods for oligoSnpSet class |
baf<- | Class '"BeadStudioSet"' |
baf<--method | Class '"BeadStudioSet"' |
baf<--method | Methods for oligoSnpSet class |
BafLrrSet-class | Class '"BeadStudioSet"' |
BafLrrSetList-class | List classes with assay data listed by chromosome |
batch | The batch variable for the samples. |
batch-method | Class "CNSet" |
batchNames | The batch variable for the samples. |
batchNames-method | Methods for class AssayData in the oligoClasses package |
batchNames-method | Class "CNSet" |
batchNames<- | The batch variable for the samples. |
batchNames<--method | Methods for class AssayData in the oligoClasses package |
batchNames<--method | Class "CNSet" |
batchStatistics | Accessor for batch statistics uses for copy number estimation and storage of model parameters |
batchStatistics-method | Class "CNSet" |
batchStatistics<- | Accessor for batch statistics uses for copy number estimation and storage of model parameters |
batchStatistics<--method | Class "CNSet" |
BeadStudioSet | Class '"BeadStudioSet"' |
BeadStudioSet-class | Class '"BeadStudioSet"' |
BeadStudioSetList-class | List classes with assay data listed by chromosome |
bothStrands | Class "AlleleSet" |
bothStrands-method | Class "AlleleSet" |
calls | Accessors and methods for SnpSet objects |
calls-method | List classes with assay data listed by chromosome |
calls-method | Class "CNSet" |
calls-method | Accessors and methods for SnpSet objects |
calls-method | Class '"SnpSet2"' |
calls-method | Methods for oligoSnpSet class |
calls<- | Accessors and methods for SnpSet objects |
calls<--method | Class "CNSet" |
calls<--method | Accessors and methods for SnpSet objects |
calls<--method | Class '"SnpSet2"' |
calls<--method | Methods for oligoSnpSet class |
callsConfidence-method | Methods for oligoSnpSet class |
callsConfidence<--method | Methods for oligoSnpSet class |
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 the appropriate function. |
checkOrder | Checks whether a eSet-derived class is ordered by chromosome and physical position |
checkOrder-method | Class '"CopyNumberSet"' |
checkOrder-method | Accessors and methods for SnpSet objects |
checkOrder-method | Container for objects with genomic annotation on SNPs |
chromosome | Methods for function chromosome in package oligoClasses |
chromosome-method | Methods for RangedSummarizedExperiment objects |
chromosome-method | Methods for function chromosome in package oligoClasses |
chromosome-method | Virtual Class for Lists of eSets |
chromosome-methods | Methods for function chromosome in package oligoClasses |
chromosome2integer | Converts chromosome to integer |
chromosome<- | Methods for function chromosome in package oligoClasses |
chromosome<--method | Methods for function chromosome in package oligoClasses |
chromosomePositionOrder | Checks whether a eSet-derived class is ordered by chromosome and physical position |
clone2 | List classes with assay data listed by chromosome |
clone2-method | List classes with assay data listed by chromosome |
close | Open and close methods for matrices and numeric vectors |
close-method | Compute average log-intensities / log-ratios |
close-method | Class "CNSet" |
close-method | Open and close methods for matrices and numeric vectors |
closeff | Open and close methods for matrices and numeric vectors |
closeff-method | Open and close methods for matrices and numeric vectors |
cnConfidence | Methods for class CopyNumberSet. |
cnConfidence-method | Class '"CopyNumberSet"' |
cnConfidence-method | Methods for oligoSnpSet class |
cnConfidence<- | Methods for class CopyNumberSet. |
cnConfidence<--method | Class '"CopyNumberSet"' |
cnConfidence<--method | Methods for oligoSnpSet class |
CNSet | Class "CNSet" |
CNSet-class | Class "CNSet" |
coerce,CNSet,oligoSnpSet | Class "CNSet" |
coerce-method | Class '"BeadStudioSet"' |
coerce-method | Class "CNSet" |
coerce-method | Class '"GenomeAnnotatedDataFrame"' |
coerce-method | Virtual Class for Lists of eSets |
coerce-method | Methods for oligoSnpSet class |
confs | Accessors and methods for SnpSet objects |
confs-method | Class "CNSet" |
confs-method | Accessors and methods for SnpSet objects |
confs-method | Class '"SnpSet2"' |
confs<- | Accessors and methods for SnpSet objects |
confs<--method | Class "CNSet" |
confs<--method | Accessors and methods for SnpSet objects |
confs<--method | Class '"SnpSet2"' |
copyNumber | Methods for class CopyNumberSet. |
copyNumber-method | Class '"BeadStudioSet"' |
copyNumber-method | List classes with assay data listed by chromosome |
copyNumber-method | Class '"CopyNumberSet"' |
copyNumber-method | Methods for oligoSnpSet class |
copyNumber<- | Methods for class CopyNumberSet. |
copyNumber<--method | Class '"BeadStudioSet"' |
copyNumber<--method | Class '"CopyNumberSet"' |
copyNumber<--method | Methods for oligoSnpSet class |
CopyNumberSet | Class '"CopyNumberSet"' |
CopyNumberSet-class | Class '"CopyNumberSet"' |
CopyNumberSet-methods | Methods for class CopyNumberSet. |
corr | Methods for class AssayData in the oligoClasses package |
corr-method | Class "CNSet" |
coverage2 | Methods for GRanges objects |
coverage2-method | Methods for GRanges objects |
createFF | Create ff objects. |
db | Get the connection to the SQLite Database |
db-method | Class "AlleleSet" |
db-method | Get the connection to the SQLite Database |
db-method | Container for objects with genomic annotation on SNPs |
db-methods | Get the connection to the SQLite Database |
DBPDInfo | Class "DBPDInfo" |
DBPDInfo-class | Class "DBPDInfo" |
delCluster | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities. |
delCluster-deprecated | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities. |
dims-method | Virtual Class for Lists of eSets |
efsExample | ExpressionFeatureSet Object |
elementLengths-method | Virtual Class for Lists of eSets |
ExonFeatureSet | "FeatureSet" and "FeatureSet" Extensions |
ExonFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
ExpressionFeatureSet | "FeatureSet" and "FeatureSet" Extensions |
ExpressionFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
ExpressionPDInfo | Class "DBPDInfo" |
ExpressionPDInfo-class | Class "DBPDInfo" |
exprs-method | Class '"SnpSet2"' |
exprs-method | Accessor for the 'exprs' slot |
exprs-methods | Accessor for the 'exprs' slot |
featureDataList | Accessor for slot 'featureDataList' in Package 'oligoClasses' ~~ |
featureDataList-method | Virtual Class for Lists of eSets |
featureDataList-methods | Accessor for slot 'featureDataList' in Package 'oligoClasses' ~~ |
FeatureSet | "FeatureSet" and "FeatureSet" Extensions |
FeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
ffdf-class | Class "ffdf" |
ff_matrix-class | Class "ff_matrix" |
ff_or_matrix-class | Class '"ff_or_matrix"' |
findOverlaps-method | Methods for GRanges objects |
flags | Batch-level summary of SNP flags. |
flags-method | Methods for class AssayData in the oligoClasses package |
flags-method | Class "CNSet" |
GeneFeatureSet | "FeatureSet" and "FeatureSet" Extensions |
GeneFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
GenericFeatureSet | "FeatureSet" and "FeatureSet" Extensions |
GenericFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
GenericPDInfo | Class "DBPDInfo" |
GenericPDInfo-class | Class "DBPDInfo" |
GenomeAnnotatedDataFrame | Class '"GenomeAnnotatedDataFrame"' |
GenomeAnnotatedDataFrame-class | Class '"GenomeAnnotatedDataFrame"' |
GenomeAnnotatedDataFrameFrom | Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses |
GenomeAnnotatedDataFrameFrom-method | Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses |
genomeBuild | Genome Build Information |
genomeBuild-method | Methods for GRanges objects |
genomeBuild-method | Container for objects with genomic annotation on SNPs |
genomeBuild-method | Virtual Class for Lists of eSets |
genomeBuild-method | Genome Build Information |
genomeBuild<- | Genome Build Information |
genomeBuild<--method | Container for objects with genomic annotation on SNPs |
genomeBuild<--method | Virtual Class for Lists of eSets |
geometry | Array Geometry Information |
geometry-method | Array Geometry Information |
getA | Compute average log-intensities / log-ratios |
getA-method | Class "AlleleSet" |
getA-method | Compute average log-intensities / log-ratios |
getArm | Container for objects with genomic annotation on SNPs |
getArm-method | Class '"GenomeAnnotatedDataFrame"' |
getArm-method | Container for objects with genomic annotation on SNPs |
getBar | Gets a bar of a given length. |
getCluster | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities. |
getCluster-deprecated | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities. |
getM | Compute average log-intensities / log-ratios |
getM-method | Class "AlleleSet" |
getM-method | Compute average log-intensities / log-ratios |
getSequenceLengths | Load chromosome sequence lengths for UCSC genome build hg18 or hg19 |
gSet | Container for objects with genomic annotation on SNPs |
gSet-class | Container for objects with genomic annotation on SNPs |
gSetList-class | Virtual Class for Lists of eSets |
i2p | Functions to convert probabilities to integers, or integers to probabilities. |
initialize-method | Class '"BeadStudioSet"' |
initialize-method | List classes with assay data listed by chromosome |
initialize-method | Class "CNSet" |
initialize-method | eSetList class |
initialize-method | Class '"CopyNumberSet"' |
initialize-method | Class "DBPDInfo" |
initialize-method | "FeatureSet" and "FeatureSet" Extensions |
initialize-method | Class '"GenomeAnnotatedDataFrame"' |
initialize-method | Class '"SnpSet2"' |
initialize-method | Class "SnpSuperSet" |
initialize-method | Container for objects with genomic annotation on SNPs |
initialize-method | Virtual Class for Lists of eSets |
initialize-method | Methods for oligoSnpSet class |
initializeBigArray | Initialize big matrices/vectors. |
initializeBigMatrix | Initialize big matrices/vectors. |
initializeBigVector | Initialize big matrices/vectors. |
integer2chromosome | Converts chromosome to integer |
integerArray | Coerce numeric matrix (or array) to a matrix (array) of integers, retaining dimnames. |
integerMatrix | Coerce numeric matrix (or array) to a matrix (array) of integers, retaining dimnames. |
is.ffmatrix | Check if object is an ff-matrix object. |
isPackageLoaded | Check if package is loaded. |
isSnp | Methods for Function isSnp in package oligoClasses~~ |
isSnp-method | Methods for RangedSummarizedExperiment objects |
isSnp-method | Methods for Function isSnp in package oligoClasses~~ |
isSnp-methods | Methods for Function isSnp in package oligoClasses~~ |
kind | Array type |
kind-method | Array type |
ldPath | Set/check large dataset options. |
ldSetOptions | Set/check large dataset options. |
ldStatus | Set/check large dataset options. |
length-method | Virtual Class for Lists of eSets |
length-method | Number of samples for FeatureSet-like objects. |
length-methods | Number of samples for FeatureSet-like objects. |
library2 | Supress package startup messages when loading a library |
list.celfiles | List CEL files. |
list_or_ffdf-class | Class "ffdf" |
locusLevelData | Basic data elements required for the HMM |
lrr | Miscellaneous generics. Methods defined in packages that depend on oligoClasses |
lrr-method | Class '"BeadStudioSet"' |
lrr-method | List classes with assay data listed by chromosome |
lrr-method | Methods for RangedSummarizedExperiment objects |
lrr<- | Class '"BeadStudioSet"' |
lrr<--method | Class '"BeadStudioSet"' |
lrr<--method | List classes with assay data listed by chromosome |
makeFeatureGRanges | Construct a GRanges object from several possible feature-level classes |
makeFeatureGRanges-method | Class '"GenomeAnnotatedDataFrame"' |
makeFeatureGRanges-method | Container for objects with genomic annotation on SNPs |
makeFeatureGRanges-method | Virtual Class for Lists of eSets |
manufacturer | Manufacturer ID for FeatureSet-like objects. |
manufacturer-method | Manufacturer ID for FeatureSet-like objects. |
manufacturer-methods | Manufacturer ID for FeatureSet-like objects. |
NgsExpressionPDInfo | Class "DBPDInfo" |
NgsExpressionPDInfo-class | Class "DBPDInfo" |
NgsTilingPDInfo | Class "DBPDInfo" |
NgsTilingPDInfo-class | Class "DBPDInfo" |
nu | Methods for class AssayData in the oligoClasses package |
nu-method | Methods for class AssayData in the oligoClasses package |
nu-method | Class "CNSet" |
numberProbes | Methods for GRanges objects |
numberProbes-method | Methods for GRanges objects |
ocLapply | lapply-like function that parallelizes code when possible. |
ocProbesets | Cluster and large dataset management utilities. |
ocSamples | Cluster and large dataset management utilities. |
oligoSet | An example instance of oligoSnpSet class |
oligoSetList-class | List classes with assay data listed by chromosome |
oligoSnpSet-class | Methods for oligoSnpSet class |
open | Open and close methods for matrices and numeric vectors |
open-method | Compute average log-intensities / log-ratios |
open-method | Class "CNSet" |
open-method | Open and close methods for matrices and numeric vectors |
openff | Open and close methods for matrices and numeric vectors |
openff-method | Open and close methods for matrices and numeric vectors |
p2i | Functions to convert probabilities to integers, or integers to probabilities. |
parStatus | Checks if oligo/crlmm can use parallel resources. |
pdPkgFromBioC | Get packages from BioConductor. |
phi | Methods for class AssayData in the oligoClasses package |
phi-method | Methods for class AssayData in the oligoClasses package |
phi-method | Class "CNSet" |
platform | Platform Information |
platform-method | Platform Information |
platform-methods | Platform Information |
pmFragmentLength | Information on Fragment Length |
pmFragmentLength-method | Information on Fragment Length |
pmFragmentLength-methods | Information on Fragment Length |
position | Methods for function position in Package oligoClasses |
position-method | Virtual Class for Lists of eSets |
position-method | Methods for function position in Package oligoClasses |
position-methods | Methods for function position in Package oligoClasses |
position<- | Class '"GenomeAnnotatedDataFrame"' |
position<--method | Class '"GenomeAnnotatedDataFrame"' |
position<--method | Methods for oligoSnpSet class |
requireAnnotation | Helper function to load packages. |
requireClusterPkg | DEPRECATED FUNCTIONS. Package loaders for clusters. |
requireClusterPkg-deprecated | DEPRECATED FUNCTIONS. Package loaders for clusters. |
requireClusterPkgSet | DEPRECATED FUNCTIONS. Package loaders for clusters. |
requireClusterPkgSet-deprecated | DEPRECATED FUNCTIONS. Package loaders for clusters. |
sampleNames-method | Methods for GRanges objects |
sampleNames-method | Virtual Class for Lists of eSets |
sampleNames-method | Sample names for FeatureSet-like objects |
sampleNames-methods | Sample names for FeatureSet-like objects |
sampleNames<--method | Virtual Class for Lists of eSets |
scqsExample | SnpCnvQSet Example |
se.exprs-method | Accessor for the 'exprs' slot |
setCluster | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities. |
setCluster-deprecated | DEPRECATED FUNCTIONS. Cluster and large dataset management utilities. |
sfsExample | SnpFeatureSet Example |
show-method | Class '"BeadStudioSet"' |
show-method | Class "CNSet" |
show-method | Class "DBPDInfo" |
show-method | "FeatureSet" and "FeatureSet" Extensions |
show-method | Container for objects with genomic annotation on SNPs |
show-method | Virtual Class for Lists of eSets |
sigma2-method | Class "CNSet" |
snpCallProbability-method | Class "CNSet" |
SnpCnvFeatureSet | "FeatureSet" and "FeatureSet" Extensions |
SnpCnvFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
SNPCNVPDInfo | Class "DBPDInfo" |
SNPCNVPDInfo-class | Class "DBPDInfo" |
SnpFeatureSet | "FeatureSet" and "FeatureSet" Extensions |
SnpFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
SNPPDInfo | Class "DBPDInfo" |
SNPPDInfo-class | Class "DBPDInfo" |
SnpSet2-class | Class '"SnpSet2"' |
SnpSuperSet | Class "SnpSuperSet" |
SnpSuperSet-class | Class "SnpSuperSet" |
splitIndicesByLength | Tools to distribute objects across nodes or by length. |
splitIndicesByNode | Tools to distribute objects across nodes or by length. |
sqsExample | SnpQSet Example |
state | Methods for GRanges objects |
state-method | Methods for GRanges objects |
tau2-method | Class "CNSet" |
TilingFeatureSet | "FeatureSet" and "FeatureSet" Extensions |
TilingFeatureSet-class | "FeatureSet" and "FeatureSet" Extensions |
TilingFeatureSet2 | "FeatureSet" and "FeatureSet" Extensions |
TilingFeatureSet2-class | "FeatureSet" and "FeatureSet" Extensions |
TilingPDInfo | Class "DBPDInfo" |
TilingPDInfo-class | Class "DBPDInfo" |
updateObject-method | Class '"BeadStudioSet"' |
updateObject-method | List classes with assay data listed by chromosome |
updateObject-method | Class "CNSet" |
updateObject-method | Class '"GenomeAnnotatedDataFrame"' |
updateObject-method | Methods for oligoSnpSet class |
$-method | Virtual Class for Lists of eSets |
$<--method | Virtual Class for Lists of eSets |
[-method | Class "CNSet" |
[-method | Virtual Class for Lists of eSets |
[[-method | List classes with assay data listed by chromosome |
[[<--method | List classes with assay data listed by chromosome |
[[<--method | Virtual Class for Lists of eSets |