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oligoClasses (version 1.34.0)

Classes for high-throughput arrays supported by oligo and crlmm

Description

This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.

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Version

Version

1.34.0

License

GPL (>= 2)

Maintainer

Benilton Carvalho

Last Published

February 15th, 2017

Functions in oligoClasses (1.34.0)

GRanges-methods

Methods for GRanges objects
GenomeAnnotatedDataFrame-class

Class "GenomeAnnotatedDataFrame"
AlleleSet-class

Class "AlleleSet"
db

Get the connection to the SQLite Database
ff_or_matrix-class

Class "ff_or_matrix"
requireAnnotation

Helper function to load packages.
chromosome-methods

Methods for function chromosome in package oligoClasses
ldSetOptions

Set/check large dataset options.
getA

Compute average log-intensities / log-ratios
BeadStudioSet-class

Class "BeadStudioSet"
celfileName

Extracts complete cel file name from a CNSet object
sfsExample

SnpFeatureSet Example
SnpSuperSet-class

Class "SnpSuperSet"
scqsExample

SnpCnvQSet Example
splitIndicesByLength

Tools to distribute objects across nodes or by length.
sampleNames-methods

Sample names for FeatureSet-like objects
gSetList-class

Virtual Class for Lists of eSets
list.celfiles

List CEL files.
assayDataList-methods

Accessor for slot assayDataList in Package oligoClasses
checkExists

Checks to see whether an object exists and, if not, executes the appropriate function.
flags

Batch-level summary of SNP flags.
integerMatrix

Coerce numeric matrix (or array) to a matrix (array) of integers, retaining dimnames.
CopyNumberSet-class

Class "CopyNumberSet"
FeatureSet-class

"FeatureSet" and "FeatureSet" Extensions
batchStatistics

Accessor for batch statistics uses for copy number estimation and storage of model parameters
ocSamples

Cluster and large dataset management utilities.
fileConnections

Open and close methods for matrices and numeric vectors
ListClasses

eSetList class
pdPkgFromBioC

Get packages from BioConductor.
featureDataList-methods

Accessor for slot featureDataList in Package oligoClasses ~~
locusLevelData

Basic data elements required for the HMM
ff_matrix-class

Class "ff_matrix"
generics

Miscellaneous generics. Methods defined in packages that depend on oligoClasses
exprs-methods

Accessor for the 'exprs' slot
i2p

Functions to convert probabilities to integers, or integers to probabilities.
makeFeatureGRanges

Construct a GRanges object from several possible feature-level classes
platform-methods

Platform Information
length-methods

Number of samples for FeatureSet-like objects.
AssayDataList

Create a list of assay data elements
pmFragmentLength-methods

Information on Fragment Length
CopyNumberSet-methods

Methods for class CopyNumberSet.
chromosome2integer

Converts chromosome to integer
manufacturer-methods

Manufacturer ID for FeatureSet-like objects.
parStatus

Checks if oligo/crlmm can use parallel resources.
affyPlatforms

Available Affymetrix platforms for SNP arrays
kind

Array type
annotationPackages

Annotation Packages
geometry

Array Geometry Information
getSequenceLengths

Load chromosome sequence lengths for UCSC genome build hg18 or hg19
initializeBigMatrix

Initialize big matrices/vectors.
isPackageLoaded

Check if package is loaded.
requireClusterPkgSet

DEPRECATED FUNCTIONS. Package loaders for clusters.
checkOrder

Checks whether a eSet-derived class is ordered by chromosome and physical position
DBPDInfo-class

Class "DBPDInfo"
oligoSnpSet-methods

Methods for oligoSnpSet class
ffdf-class

Class "ffdf"
CNSet-class

Class "CNSet"
GenomeAnnotatedDataFrameFrom-methods

Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses
BeadStudioSetList-class

List classes with assay data listed by chromosome
setCluster

DEPRECATED FUNCTIONS. Cluster and large dataset management utilities.
genomeBuild

Genome Build Information
gSet-class

Container for objects with genomic annotation on SNPs
position-methods

Methods for function position in Package oligoClasses
AssayData-methods

Methods for class AssayData in the oligoClasses package
celfileDate

Cel file dates
SummarizedExperiment-methods

Methods for RangedSummarizedExperiment objects
efsExample

ExpressionFeatureSet Object
Deprecated

oligoClasses Deprecated
is.ffmatrix

Check if object is an ff-matrix object.
SnpSet-methods

Accessors and methods for SnpSet objects
library2

Supress package startup messages when loading a library
SnpSet2-class

Class "SnpSet2"
batch

The batch variable for the samples.
sqsExample

SnpQSet Example
createFF

Create ff objects.
oligoSet

An example instance of oligoSnpSet class
ocLapply

lapply-like function that parallelizes code when possible.
isSnp-methods

Methods for Function isSnp in package oligoClasses~~
getBar

Gets a bar of a given length.