R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
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Classification

Results 1 - 10 of 73 found.
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AlleleSet-class (Package: oligoClasses) : Class "AlleleSet"

A class for storing the locus-level summaries of the normalized intensities

● Data Source: BioConductor
● Keywords: classes
● Alias: AlleleSet, AlleleSet-class, allele, allele,AlleleSet-method, allele,SnpFeatureSet-method, bothStrands, bothStrands,AlleleSet-method, bothStrands,SnpFeatureSet-method, db,AlleleSet-method, getA,AlleleSet-method, getM,AlleleSet-method
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getA (Package: oligoClasses) : Compute average log-intensities / log-ratios

Methods to compute average log-intensities and log-ratios across alleles, within strand.

● Data Source: BioConductor
● Keywords: manip
● Alias: getA, getA,SnpCnvQSet-method, getA,SnpQSet-method, getA,TilingFeatureSet2-method, getM, getM,SnpCnvQSet-method, getM,SnpQSet-method, getM,TilingFeatureSet2-method
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AssayData-methods (Package: oligoClasses) : Methods for class AssayData in the oligoClasses package

Batch statistics used for estimating copy number are stored as AssayData in the 'batchStatistics' slot of the CNSet class. Each element in the AssayData must have the same number of rows and columns. Rows correspond to features and columns correspond to batch.

● Data Source: BioConductor
● Keywords: classes
● Alias: batchNames,AssayData-method, batchNames<-,AssayData-method, corr, flags,AssayData-method, nu, nu,AssayData,character-method, phi, phi,AssayData,character-method
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AssayDataList (Package: oligoClasses) : Create a list of assay data elements

The eSetList-derived classes have an assayDataList slot instead of an assayData slot.

● Data Source: BioConductor
● Keywords: manip
● Alias: AssayDataList
● 0 images

BeadStudioSet-class (Package: oligoClasses) : Class code{"BeadStudioSet"

A container for log R ratios and B allele frequencies from SNP arrays.

● Data Source: BioConductor
● Keywords: classes
● Alias: BafLrrSet-class, BeadStudioSet, BeadStudioSet-class, baf,BeadStudioSet-method, baf<-, baf<-,BeadStudioSet-method, 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
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BeadStudioSetList-class (Package: oligoClasses) : List classes with assay data listed by chromosome

Container for log R ratios and B allele frequencies stored by chromosome.

● Data Source: BioConductor
● Keywords: classes
● Alias: BafLrrSetList-class, BeadStudioSetList-class, [[,BafLrrSetList,ANY,ANY-method, [[,BeadStudioSetList,ANY,ANY-method, [[<-,BafLrrSetList,ANY,ANY,BafLrrSet-method, baf,BafLrrSetList-method, baf,BeadStudioSetList-method, baf,oligoSetList-method, 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
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CNSet-class (Package: oligoClasses) : Class "CNSet"

CNSet is a container for intermediate data and parameters pertaining to allele-specific copy number estimation. Methods for CNSet objects, including accessors for linear model parameters and allele-specific copy number are included here.

● Data Source: BioConductor
● Keywords: classes
● Alias: A,CNSet-method, A<-,CNSet-method, B,CNSet-method, B<-,CNSet-method, CNSet, CNSet-class, [,CNSet,ANY-method, [,CNSet-method, allele,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, 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
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ListClasses (Package: oligoClasses) : eSetList class

Initialization method for eSetList virtual class.

● Data Source: BioConductor
● Keywords: classes
● Alias: initialize,eSetList-method
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CopyNumberSet-class (Package: oligoClasses) : Class code{"CopyNumberSet"

Container for storing total copy number estimates and confidence scores of the copy number estimates.

● Data Source: BioConductor
● Keywords: classes
● Alias: CopyNumberSet, CopyNumberSet-class, checkOrder,CopyNumberSet-method, cnConfidence,CopyNumberSet-method, cnConfidence<-,CopyNumberSet,matrix-method, copyNumber,CopyNumberSet-method, copyNumber<-,CopyNumberSet,matrix-method, initialize,CopyNumberSet-method
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CopyNumberSet-methods (Package: oligoClasses) : Methods for class CopyNumberSet.

Accessors and CopyNumberSet

● Data Source: BioConductor
● Keywords: manip, methods
● Alias: CopyNumberSet-methods, cnConfidence, cnConfidence<-, copyNumber, copyNumber<-
● 0 images