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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 SummarizedExperiment 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 SummarizedExperiment 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 |
| clone | List classes with assay data listed by chromosome |
| clone-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 |
| 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 SummarizedExperiment 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 SummarizedExperiment 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 |