Classes and Methods for high throughput SNP chip data


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Documentation for package ‘SNPchip’ version 1.4.0

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A C D E F G H I P R S U

$,ParESet-method Class "ParESet"
$<-,ParESet-method Class "ParESet"

-- A --

addFeatureData Method for Function addFeatureData
addFeatureData,eSet-method Method for Function addFeatureData
addFeatureData-methods Method for Function addFeatureData
alleleA Accessor for the A allele
alleleA,AnnotatedDataFrame-method Accessor for the A allele
alleleA,SnpLevelSet-method Accessor for the A allele
alleleB Accessor for the B allele
alleleB,AnnotatedDataFrame-method Accessor for the B allele
alleleB,SnpLevelSet-method Accessor for the B allele

-- C --

centromere Coordinates of centromere
chromosome Accessors for feature-level SNP annotation
chromosome,AnnotatedDataFrame-method Accessors for feature-level SNP annotation
chromosome,oligoSnpSet-method Accessors for feature-level SNP annotation
chromosome,SnpCallSet-method Accessors for feature-level SNP annotation
chromosome,SnpCopyNumberSet-method Accessors for feature-level SNP annotation
chromosome,SnpLevelSet-method Accessors for feature-level SNP annotation
chromosome-methods Accessors for feature-level SNP annotation
chromosome2numeric Converts chromosome to numeric
chromosomeAnnotation chromosome annotation
chromosomeSize Get size of chromosome in number of base pairs.
cnConfidence,RatioSnpSet-method Accessors for RatioSnpSet objects
cnConfidence<-,RatioSnpSet,matrix-method Accessors for RatioSnpSet objects
coerce,AnnotatedSnpCallSet,SnpCallSet-method Methods for Function coerce
coerce,AnnotatedSnpCopyNumberSet,SnpCopyNumberSet-method Methods for Function coerce
coerce,AnnotatedSnpSet,oligoSnpSet-method Methods for Function coerce
coerce,oligoSnpSet,SnpCallSet-method Methods for Function coerce
coerce,oligoSnpSet,SnpCopyNumberSet-method Methods for Function coerce
coerce-methods Methods for Function coerce
copyNumber,RatioSnpSet-method Accessors for RatioSnpSet objects
copyNumber<-,RatioSnpSet,matrix-method Accessors for RatioSnpSet objects
crlmmOut A data object created by the oligo vignette
cytoband Start and stop sites of cytoband

-- D --

dbSnpId The dbSNP identifier
dbSnpId,AnnotatedDataFrame-method The dbSNP identifier
dbSnpId,SnpLevelSet-method The dbSNP identifier

-- E --

enzyme Enzyme used to digest DNA
enzyme,AnnotatedDataFrame-method Enzyme used to digest DNA
enzyme,SnpLevelSet-method Enzyme used to digest DNA

-- F --

fragmentLength Accessor for the fragment length
fragmentLength,AnnotatedDataFrame-method Accessor for the fragment length
fragmentLength,SnpLevelSet-method Accessor for the fragment length

-- G --

getPar Adds graphical parameters for plotting SNP data
getPar,ParESet-method Adds graphical parameters for plotting SNP data

-- H --

hapmap Data from the hapmap project
hmmPredict Accessor for HMM output
hmmPredict,ParESet-method Class "ParESet"
HmmPredict-class Class for containing output from a hidden Markov fit to SNP-level data of genotype calls and copy number estimates

-- I --

initialize,ParESet-method Class "ParESet"
initialize,ParSnpCallSet-method Class "ParSnpCallSet"
initialize,ParSnpCopyNumberSet-method Class "ParSnpCopyNumberSet"
initialize,ParSnpSet-method Class "ParSnpSet"
initialize,RatioSnpSet-method Accessors for RatioSnpSet objects

-- P --

ParESet-class Class "ParESet"
ParSnpCallSet-class Class "ParSnpCallSet"
ParSnpCopyNumberSet-class Class "ParSnpCopyNumberSet"
ParSnpSet-class Class "ParSnpSet"
plotCytoband Plots cytoband for one chromosome
plotPredictions Plots the predictions from the HMM
plotSnp Plots copy number and genotype calls against physical position
plotSnp,ParESet,SnpLevelSet-method Class "ParESet"
plotSnp,ParSnpCallSet,SnpCallSet-method Plots copy number and genotype calls against physical position
plotSnp,ParSnpCopyNumberSet,SnpCopyNumberSet-method Plots copy number and genotype calls against physical position
plotSnp,ParSnpSet,oligoSnpSet-method Plots copy number and genotype calls against physical position
plotSnp,SnpLevelSet-method Plots copy number and genotype calls against physical position
position Accessors for feature-level SNP annotation
position,AnnotatedDataFrame-method Accessors for feature-level SNP annotation
position,oligoSnpSet-method Accessors for feature-level SNP annotation
position,SnpCallSet-method Accessors for feature-level SNP annotation
position,SnpCopyNumberSet-method Accessors for feature-level SNP annotation
position,SnpLevelSet-method Accessors for feature-level SNP annotation
position-methods Accessors for feature-level SNP annotation

-- R --

ratio Accessors for RatioSnpSet objects
ratio,RatioSnpSet-method Accessors for RatioSnpSet objects
ratio,SnpLevelSet-method Accessors for RatioSnpSet objects
ratio<-,SnpLevelSet,matrix-method Accessors for RatioSnpSet objects
ratioConfidence Accessors for RatioSnpSet objects
ratioConfidence,RatioSnpSet-method Accessors for RatioSnpSet objects
ratioConfidence<-,RatioSnpSet,matrix-method Accessors for RatioSnpSet objects
RatioSnpSet-class Class for high throughput SNP-level data. The assay data contains ratios of copy number.
RatioSnpSet-methods Accessors for RatioSnpSet objects

-- S --

sample.snpset Example object of class oligoSnpSet
selectSomeIndex Method from Biobase for selecting indices
selectSomeIndex,data.frame-method Method from Biobase for selecting indices
show,oligoSnpSet-method show methods
show,ParESet-method show methods
show,ParSnpCallSet-method show methods
show,ParSnpCopyNumberSet-method show methods
show,ParSnpSet-method show methods
show-methods show methods
showSummary Displays descriptive statistics for a sample.
smoothSnp A simple nonparametric smoother for genotype and copy number
smoothSnp,oligoSnpSet-method A simple nonparametric smoother for genotype and copy number
snpPar Accessor for graphical parameters
snpPar,ParESet-method Class "ParESet"
snpPar<-,ParESet-method Class "ParESet"
snpset Accessor for SNP data
snpset,ParESet-method Class "ParESet"
summary,AnnotatedSnpSet-method Methods for Function summary
summary,ANY-method Methods for Function summary
summary,oligoSnpSet-method Methods for Function summary
summary,SnpCallSet-method Methods for Function summary
summary-methods Methods for Function summary

-- U --

updateObject,oligoSnpSet-method updateObject methods