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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
1.32.0
1.30.0
1.28.0
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Version
1.34.0
License
GPL (>= 2)
Maintainer
Benilton Carvalho
Last Published
January 1st, 1970
Functions in oligoClasses (1.34.0)
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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.