Man pages for jmacdon/oligoClasses
Classes for high-throughput arrays supported by oligo and crlmm
| 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 |
