Package: oligoClasses 1.69.0
Benilton Carvalho
oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm
This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.
Authors:
oligoClasses_1.69.0.tar.gz
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oligoClasses.pdf |oligoClasses.html✨
oligoClasses/json (API)
NEWS
| # Install 'oligoClasses' in R: |
| install.packages('oligoClasses', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- efsExample - ExpressionFeatureSet Object
- locusLevelData - Basic data elements required for the HMM
- oligoSet - An example instance of oligoSnpSet class
- scqsExample - SnpCnvQSet Example
- sfsExample - SnpFeatureSet Example
- sqsExample - SnpQSet Example
On BioConductor:oligoClasses-1.69.0(bioc 3.21)oligoClasses-1.68.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:37e0a0eeed. Checks:OK: 1 ERROR: 1 WARNING: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 29 2024 |
| R-4.5-win | WARNING | Nov 29 2024 |
| R-4.5-linux | ERROR | Dec 29 2024 |
| R-4.4-win | WARNING | Nov 29 2024 |
| R-4.4-mac | WARNING | Dec 29 2024 |
| R-4.3-win | WARNING | Nov 29 2024 |
| R-4.3-mac | WARNING | Dec 29 2024 |
Exports:AA<-affyPlatformsalleleannotatedDataFrameFromannotationannotationPackagesassayDataListAssayDataListBB<-bafbaf<-batchbatchNamesbatchNames<-batchStatisticsbatchStatistics<-bothStrandscallscalls<-celfileDatecelfileNamecheckExistscheckOrderchromosomechromosome<-chromosome2integerchromosomePositionOrderclone2closecloseffcnConfidencecnConfidence<-coerceconfsconfs<-copyNumbercopyNumber<-coverage2createFFdbdelClusterdimselementNROWSexprsfeatureDataListfeaturesInRangefindOverlapsflagsGenomeAnnotatedDataFrameFromgenomeBuildgenomeBuild<-geometrygetAgetArmgetBargetClustergetMgetSequenceLengthsi2pinitializeinitializeBigArrayinitializeBigMatrixinitializeBigVectorinteger2chromosomeintegerArrayintegerMatrixis.ffmatrixisPackageLoadedisSnpkindldPathldSetOptionsldStatuslibrary2list.celfileslrrlrr<-makeFeatureGRangesmanufacturermeannunumberProbesocLapplyocProbesetsocSamplesopenopenffp2iparStatuspdPkgFromBioCphipositionposition<-requireAnnotationrequireClusterPkgrequireClusterPkgSetsampleNamessampleNames<-setClustershowsplitIndicesByLengthsplitIndicesByNodestateupdateObject
Dependencies:abindaffyioaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapffforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesiteratorsjsonlitelatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrR6rlangRSQLiteS4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Available Affymetrix platforms for SNP arrays | affyPlatforms |
| Class "AlleleSet" | allele allele,AlleleSet-method allele,SnpFeatureSet-method AlleleSet AlleleSet-class bothStrands bothStrands,AlleleSet-method bothStrands,SnpFeatureSet-method db,AlleleSet-method getA,AlleleSet-method getM,AlleleSet-method |
| Annotation Packages | annotationPackages |
| Methods for class AssayData in the oligoClasses package | batchNames,AssayData-method batchNames<-,AssayData-method corr flags,AssayData-method nu nu,AssayData,character-method phi phi,AssayData,character-method |
| Create a list of assay data elements | AssayDataList |
| Accessor for slot assayDataList in Package 'oligoClasses' | assayDataList assayDataList,oligoSetList-method assayDataList-methods |
| The batch variable for the samples. | batch batchNames batchNames<- |
| Accessor for batch statistics uses for copy number estimation and storage of model parameters | batchStatistics batchStatistics<- |
| Class '"BeadStudioSet"' | baf,BeadStudioSet-method baf<- baf<-,BeadStudioSet-method BafLrrSet-class BeadStudioSet BeadStudioSet-class coerce,BeadStudioSet,data.frame-method copyNumber,BeadStudioSet-method copyNumber<-,BeadStudioSet,ANY-method initialize,BeadStudioSet-method lrr,BeadStudioSet-method lrr<- lrr<-,BafLrrSet,ANY-method lrr<-,BafLrrSet-method lrr<-,BeadStudioSet,ANY-method lrr<-,BeadStudioSet-method show,BeadStudioSet-method updateObject,BeadStudioSet-method |
| List classes with assay data listed by chromosome | baf,BafLrrSetList-method baf,BeadStudioSetList-method baf,oligoSetList-method BafLrrSetList-class BeadStudioSetList-class calls,oligoSetList-method clone2 clone2,BafLrrSetList-method copyNumber,oligoSetList-method initialize,BeadStudioSetList-method lrr,BafLrrSetList-method lrr,BeadStudioSetList-method lrr<-,BafLrrSetList,matrix-method oligoSetList-class updateObject,BeadStudioSetList-method [[,BafLrrSetList,ANY,ANY-method [[,BeadStudioSetList,ANY,ANY-method [[<-,BafLrrSetList,ANY,ANY,BafLrrSet-method |
| Cel file dates | celfileDate |
| Extracts complete cel file name from a CNSet object | celfileName |
| Checks to see whether an object exists and, if not, executes the appropriate function. | checkExists |
| Checks whether a eSet-derived class is ordered by chromosome and physical position | checkOrder chromosomePositionOrder |
| Methods for function chromosome in package oligoClasses | chromosome chromosome,AnnotatedDataFrame-method chromosome,GenomeAnnotatedDataFrame-method chromosome,GRanges-method chromosome,GRangesList-method chromosome,gSet-method chromosome,SnpSet-method chromosome-methods chromosome<- chromosome<-,GenomeAnnotatedDataFrame,integer-method chromosome<-,gSet,integer-method chromosome<-,SnpSet,integer-method |
| Converts chromosome to integer | chromosome2integer integer2chromosome |
| Class "CNSet" | A,CNSet-method A<-,CNSet-method allele,CNSet-method B,CNSet-method B<-,CNSet-method batch,CNSet-method batchNames,CNSet-method batchNames<-,CNSet-method batchStatistics,CNSet-method batchStatistics<-,CNSet,AssayData-method calls,CNSet-method calls<-,CNSet,matrix-method close,CNSet-method CNSet CNSet-class coerce,CNSet,CopyNumberSet-method coerce,CNSet,oligoSnpSet coerce,CNSet,oligoSnpSet-method coerce,CNSetLM,CNSet-method confs,CNSet-method confs<-,CNSet,matrix-method corr,CNSet,character-method flags,CNSet-method initialize,CNSet-method initialize,CNSetLM-method nu,CNSet,character-method open,CNSet-method phi,CNSet,character-method show,CNSet-method sigma2,CNSet,character-method snpCallProbability,CNSet-method tau2,CNSet,character-method updateObject,CNSet-method [,CNSet,ANY-method [,CNSet-method |
| Class '"CopyNumberSet"' | checkOrder,CopyNumberSet-method cnConfidence,CopyNumberSet-method cnConfidence<-,CopyNumberSet,matrix-method copyNumber,CopyNumberSet-method copyNumber<-,CopyNumberSet,matrix-method CopyNumberSet CopyNumberSet-class initialize,CopyNumberSet-method |
| Methods for class CopyNumberSet. | cnConfidence cnConfidence<- copyNumber copyNumber<- CopyNumberSet-methods |
| Create ff objects. | createFF |
| Get the connection to the SQLite Database | db db,DBPDInfo-method db,FeatureSet-method db,SnpCnvQSet-method db,SnpQSet-method db,SnpSet-method db-methods |
| Class "DBPDInfo" | AffyExonPDInfo AffyExonPDInfo-class AffyExpressionPDInfo AffyExpressionPDInfo-class AffyGenePDInfo AffyGenePDInfo-class AffySNPCNVPDInfo AffySNPCNVPDInfo-class AffySNPPDInfo AffySNPPDInfo-class AffySTPDInfo AffySTPDInfo-class AffyTilingPDInfo AffyTilingPDInfo-class annotation,DBPDInfo-method DBPDInfo DBPDInfo-class ExpressionPDInfo ExpressionPDInfo-class GenericPDInfo GenericPDInfo-class initialize,DBPDInfo-method NgsExpressionPDInfo NgsExpressionPDInfo-class NgsTilingPDInfo NgsTilingPDInfo-class show,DBPDInfo-method SNPCNVPDInfo SNPCNVPDInfo-class SNPPDInfo SNPPDInfo-class TilingPDInfo TilingPDInfo-class |
| ExpressionFeatureSet Object | efsExample |
| Accessor for the 'exprs' slot | exprs,FeatureSet-method exprs-methods se.exprs,FeatureSet-method |
| Accessor for slot 'featureDataList' in Package 'oligoClasses' ~~ | featureDataList featureDataList-methods |
| "FeatureSet" and "FeatureSet" Extensions | ExonFeatureSet ExonFeatureSet-class ExpressionFeatureSet ExpressionFeatureSet-class FeatureSet FeatureSet-class GeneFeatureSet GeneFeatureSet-class GenericFeatureSet GenericFeatureSet-class initialize,FeatureSet-method show,FeatureSet-method SnpCnvFeatureSet SnpCnvFeatureSet-class SnpFeatureSet SnpFeatureSet-class TilingFeatureSet TilingFeatureSet-class TilingFeatureSet2 TilingFeatureSet2-class |
| Class "ff_matrix" | annotatedDataFrameFrom,ff_matrix-method ff_matrix-class |
| Class '"ff_or_matrix"' | ff_or_matrix-class |
| Class "ffdf" | ffdf-class list_or_ffdf-class |
| Open and close methods for matrices and numeric vectors | close close,array-method close,matrix-method close,numeric-method closeff closeff,CNSet-method open open,array-method open,matrix-method open,numeric-method openff openff,CNSet-method |
| Batch-level summary of SNP flags. | flags |
| Miscellaneous generics. Methods defined in packages that depend on oligoClasses | baf lrr |
| Class '"GenomeAnnotatedDataFrame"' | coerce,AnnotatedDataFrame,GenomeAnnotatedDataFrame-method GenomeAnnotatedDataFrame GenomeAnnotatedDataFrame-class getArm,GenomeAnnotatedDataFrame-method initialize,GenomeAnnotatedDataFrame-method makeFeatureGRanges,GenomeAnnotatedDataFrame-method position<- position<-,GenomeAnnotatedDataFrame,integer-method updateObject,GenomeAnnotatedDataFrame-method |
| Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses | GenomeAnnotatedDataFrameFrom GenomeAnnotatedDataFrameFrom,array-method GenomeAnnotatedDataFrameFrom,AssayData-method GenomeAnnotatedDataFrameFrom,ff_or_matrix-method GenomeAnnotatedDataFrameFrom,list-method GenomeAnnotatedDataFrameFrom,NULL-method |
| Genome Build Information | genomeBuild genomeBuild,DBPDInfo-method genomeBuild,FeatureSet-method genomeBuild<- |
| Array Geometry Information | geometry geometry,DBPDInfo-method geometry,FeatureSet-method |
| Compute average log-intensities / log-ratios | A A,AlleleSet-method A<- A<-,AlleleSet,matrix-method A<-,AlleleSet-method B B,AlleleSet-method B<- B<-,AlleleSet,matrix-method B<-,AlleleSet-method close,AlleleSet-method getA getA,SnpCnvQSet-method getA,SnpQSet-method getA,TilingFeatureSet2-method getM getM,SnpCnvQSet-method getM,SnpQSet-method getM,TilingFeatureSet2-method open,AlleleSet-method |
| Gets a bar of a given length. | getBar |
| Load chromosome sequence lengths for UCSC genome build hg18 or hg19 | getSequenceLengths |
| Methods for GRanges objects | coverage2 coverage2,GRanges-method coverage2,GRangesList-method findOverlaps,GRanges,gSet-method findOverlaps,GRangesList,gSet-method genomeBuild,GRanges-method numberProbes numberProbes,GRanges-method numberProbes,GRangesList-method sampleNames,GRanges-method sampleNames,GRangesList-method state state,GRanges-method state,GRangesList-method |
| Container for objects with genomic annotation on SNPs | checkOrder,gSet-method db,gSet-method genomeBuild,gSet-method genomeBuild<-,gSet,character-method getArm getArm,gSet-method gSet gSet-class initialize,gSet-method makeFeatureGRanges,gSet-method show,gSet-method |
| Virtual Class for Lists of eSets | $,gSetList-method $<-,gSetList-method annotation,gSetList-method assayDataList,gSetList-method chromosome,gSetList-method coerce,gSetList,list-method dims,gSetList-method elementNROWS,gSetList-method featureDataList,gSetList-method genomeBuild,gSetList-method genomeBuild<-,gSetList,character-method gSetList-class initialize,gSetList-method length,gSetList-method makeFeatureGRanges,gSetList-method position,gSetList-method sampleNames,gSetList-method sampleNames<-,gSetList,character-method show,gSetList-method [,gSetList,ANY-method [,gSetList-method [[<-,gSetList,ANY,ANY,BafLrrSet-method |
| Functions to convert probabilities to integers, or integers to probabilities. | i2p p2i |
| Initialize big matrices/vectors. | initializeBigArray initializeBigMatrix initializeBigVector |
| Coerce numeric matrix (or array) to a matrix (array) of integers, retaining dimnames. | integerArray integerMatrix |
| Check if object is an ff-matrix object. | is.ffmatrix |
| Check if package is loaded. | isPackageLoaded |
| Methods for Function isSnp in package oligoClasses~~ | isSnp isSnp,character-method isSnp,GenomeAnnotatedDataFrame-method isSnp,gSet-method isSnp,SnpSet-method isSnp-methods |
| Array type | kind kind,AffyExonPDInfo-method kind,AffyExpressionPDInfo-method kind,AffyGenePDInfo-method kind,AffyHTAPDInfo-method kind,AffySNPCNVPDInfo-method kind,AffySNPPDInfo-method kind,ExpressionPDInfo-method kind,FeatureSet-method kind,GenericPDInfo-method kind,TilingPDInfo-method |
| Set/check large dataset options. | ldPath ldSetOptions ldStatus |
| Number of samples for FeatureSet-like objects. | length,FeatureSet-method length-methods |
| Supress package startup messages when loading a library | library2 |
| List CEL files. | list.celfiles |
| eSetList class | initialize,eSetList-method |
| Basic data elements required for the HMM | locusLevelData |
| Construct a GRanges object from several possible feature-level classes | makeFeatureGRanges |
| Manufacturer ID for FeatureSet-like objects. | manufacturer manufacturer,DBPDInfo-method manufacturer,FeatureSet-method manufacturer-methods |
| lapply-like function that parallelizes code when possible. | ocLapply |
| Cluster and large dataset management utilities. | ocProbesets ocSamples |
| An example instance of oligoSnpSet class | oligoSet |
| Methods for oligoSnpSet class | baf,oligoSnpSet-method baf<-,oligoSnpSet-method calls,oligoSnpSet-method calls<-,oligoSnpSet,matrix-method callsConfidence,oligoSnpSet-method callsConfidence<-,oligoSnpSet,matrix-method cnConfidence,oligoSnpSet-method cnConfidence<-,oligoSnpSet,matrix-method coerce,oligoSnpSet,data.frame-method copyNumber,oligoSnpSet-method copyNumber<-,oligoSnpSet,matrix-method initialize,oligoSnpSet-method oligoSnpSet-class position<-,oligoSnpSet,integer-method updateObject,oligoSnpSet-method |
| Checks if oligo/crlmm can use parallel resources. | parStatus |
| Get packages from BioConductor. | pdPkgFromBioC |
| Platform Information | platform platform,FeatureSet-method platform-methods |
| Information on Fragment Length | pmFragmentLength pmFragmentLength,AffySNPPDInfo-method pmFragmentLength-methods |
| Methods for function position in Package oligoClasses | position position,AnnotatedDataFrame-method position,GenomeAnnotatedDataFrame-method position,gSet-method position,SnpSet-method position-methods |
| Helper function to load packages. | requireAnnotation |
| DEPRECATED FUNCTIONS. Package loaders for clusters. | requireClusterPkg requireClusterPkg-deprecated requireClusterPkgSet requireClusterPkgSet-deprecated |
| Sample names for FeatureSet-like objects | sampleNames,FeatureSet-method sampleNames-methods |
| SnpCnvQSet Example | scqsExample |
| DEPRECATED FUNCTIONS. Cluster and large dataset management utilities. | delCluster delCluster-deprecated getCluster getCluster-deprecated setCluster setCluster-deprecated |
| SnpFeatureSet Example | sfsExample |
| Accessors and methods for SnpSet objects | calls calls,SnpSet-method calls<- calls<-,SnpSet,matrix-method checkOrder,SnpSet-method confs confs,SnpSet-method confs<- confs<-,SnpSet,matrix-method |
| Class '"SnpSet2"' | calls,SnpSet2-method calls<-,SnpSet2,matrix-method confs,SnpSet2-method confs<-,SnpSet2,matrix-method exprs,SnpSet2-method initialize,SnpSet2-method SnpSet2-class |
| Class "SnpSuperSet" | initialize,SnpSuperSet-method SnpSuperSet SnpSuperSet-class |
| Tools to distribute objects across nodes or by length. | splitIndicesByLength splitIndicesByNode |
| SnpQSet Example | sqsExample |
| Methods for RangedSummarizedExperiment objects | baf,RangedSummarizedExperiment-method baf,SummarizedExperiment-method chromosome,RangedSummarizedExperiment-method chromosome,SummarizedExperiment-method isSnp,RangedSummarizedExperiment-method isSnp,SummarizedExperiment-method lrr,RangedSummarizedExperiment-method lrr,SummarizedExperiment-method |
