Package: oligoClasses 1.67.0

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:Benilton Carvalho and Robert Scharpf

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oligoClasses.pdf |oligoClasses.html✨
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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-1.67.0(bioc 3.20)oligoClasses-1.66.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

106 exports 3.33 score 51 dependencies 19 dependents 3 mentions

Last updated 2 months agofrom:46ee6a9326

Exports:A A<-affyPlatforms allele annotatedDataFrameFrom annotation annotationPackages assayDataList AssayDataList B B<-baf baf<-batch batchNames batchNames<-batchStatistics batchStatistics<-bothStrands calls calls<-celfileDate celfileName checkExists checkOrder chromosome chromosome<-chromosome2integer chromosomePositionOrder clone2 close closeff cnConfidence cnConfidence<-coerce confs confs<-copyNumber copyNumber<-coverage2 createFF db delCluster dims elementNROWS exprs featureDataList featuresInRange findOverlaps flags GenomeAnnotatedDataFrameFrom genomeBuild genomeBuild<-geometry getA getArm getBar getCluster getM getSequenceLengths i2p initialize initializeBigArray initializeBigMatrix initializeBigVector integer2chromosome integerArray integerMatrix is.ffmatrix isPackageLoaded isSnp kind ldPath ldSetOptions ldStatus library2 list.celfiles lrr lrr<-makeFeatureGRanges manufacturer mean nu numberProbes ocLapply ocProbesets ocSamples open openff p2i parStatus pdPkgFromBioC phi position position<-requireAnnotation requireClusterPkg requireClusterPkgSet sampleNames sampleNames<-setCluster show splitIndicesByLength splitIndicesByNode state updateObject

Dependencies:abind affyio askpass Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap ff foreach GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges iterators jsonlite lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr R6 rlang RSQLite S4Arrays S4Vectors SparseArray SummarizedExperiment sys UCSC.utils vctrs XVector zlibbioc

Citation

Development and contributors

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