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

affyPlatformsAvailable Affymetrix platforms for SNP arrays
AlleleSet-classClass "AlleleSet"
AlleleSet-methodsCompute average log-intensities / log-ratios
annotationPackagesAnnotation Packages
AssayDataListCreate a list of assay data elements
assayDataList-methodsAccessor for slot assayDataList in Package 'oligoClasses'
AssayData-methodsMethods for class AssayData in the oligoClasses package
batchThe batch variable for the samples.
batchStatisticsAccessor for batch statistics uses for copy number estimation...
BeadStudioSet-classClass '"BeadStudioSet"'
BeadStudioSetList-classList classes with assay data listed by chromosome
celfileDateCel file dates
celfileNameExtracts complete cel file name from a CNSet object
checkExistsChecks to see whether an object exists and, if not, executes...
checkOrderChecks whether a eSet-derived class is ordered by chromosome...
chromosome2integerConverts chromosome to integer
chromosome-methodsMethods for function chromosome in package oligoClasses
ClassesNotExportedeSetList class
clusterOptsCluster and large dataset management utilities.
clusterOptsDeprecatedDEPRECATED FUNCTIONS. Cluster and large dataset management...
CNSet-classClass "CNSet"
CopyNumberSet-classClass '"CopyNumberSet"'
CopyNumberSet-methodsMethods for class CopyNumberSet.
createFFCreate ff objects.
data-efsExampleExpressionFeatureSet Object
data-scqsExampleSnpCnvQSet Example
data-sfsExampleSnpFeatureSet Example
data-sqsExampleSnpQSet Example
dbGet the connection to the SQLite Database
DBPDInfo-classClass "DBPDInfo"
defunctoligoClasses Deprecated
exprs-methodsAccessor for the 'exprs' slot
featureDataList-methodsAccessor for slot 'featureDataList' in Package 'oligoClasses'...
FeatureSetExtensions-class"FeatureSet" and "FeatureSet" Extensions
ffdfClass "ffdf"
ff_matrixClass "ff_matrix"
ff_or_matrix-classClass '"ff_or_matrix"'
fileConnectionsOpen and close methods for matrices and numeric vectors
flagsBatch-level summary of SNP flags.
genericsMiscellaneous generics. Methods defined in packages that...
GenomeAnnotatedDataFrame-classClass '"GenomeAnnotatedDataFrame"'
GenomeAnnotatedDataFrameFrom-methodsMethods for Function GenomeAnnotatedDataFrameFrom in Package...
genomeBuildGenome Build Information
geometry-methodsArray Geometry Information
getBarGets a bar of a given length.
getSequenceLengthsLoad chromosome sequence lengths for UCSC genome build hg18...
GRanges-methodsMethods for GRanges objects
gSet-classContainer for objects with genomic annotation on SNPs
gSetList-classVirtual Class for Lists of eSets
i2p_p2iFunctions to convert probabilities to integers, or integers...
integerMatrixCoerce numeric matrix (or array) to a matrix (array) of...
is.ffmatrixCheck if object is an ff-matrix object.
isPackageLoadedCheck if package is loaded.
isSnp-methodsMethods for Function isSnp in package oligoClasses~~
kindArray type
largeObjectsInitialize big matrices/vectors.
ldOptsSet/check large dataset options.
length-methodsNumber of samples for FeatureSet-like objects.
library2Supress package startup messages when loading a library
list.celfilesList CEL files.
locusLevelDataBasic data elements required for the HMM
makeFeatureGRangesConstruct a GRanges object from several possible...
manufacturer-methodsManufacturer ID for FeatureSet-like objects.
ocLapplylapply-like function that parallelizes code when possible.
oligoSetExampleAn example instance of oligoSnpSet class
oligoSnpSet-methodsMethods for oligoSnpSet class
parStatusChecks if oligo/crlmm can use parallel resources.
pdPkgFromBioCGet packages from BioConductor.
platform-methodsPlatform Information
pmFragmentLength-methodsInformation on Fragment Length
position-methodsMethods for function position in Package oligoClasses
requireAnnotationHelper function to load packages.
requireClusterPkgSetDeprecatedDEPRECATED FUNCTIONS. Package loaders for clusters.
sampleNames-methodsSample names for FeatureSet-like objects
SnpSet2-classClass '"SnpSet2"'
SnpSet-methodsAccessors and methods for SnpSet objects
SnpSuperSet-classClass "SnpSuperSet"
splitVecTools to distribute objects across nodes or by length.
SummarizedExperiment-methodsMethods for RangedSummarizedExperiment objects
oligoClasses documentation built on Nov. 17, 2017, 10:21 a.m.