Classes and Methods for high throughput SNP chip data


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Documentation for package ‘SNPchip’ version 1.10.0

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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
chromosome2integer Converts chromosome to integer or vice versa
chromosomeAnnotation chromosome annotation
chromosomeSize 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
integer2chromosome Converts chromosome to integer or vice versa

-- P --

ParESet-class Class "ParESet"
ParSnpCallSet-class Class "ParSnpCallSet"
ParSnpCopyNumberSet-class Class "ParSnpCopyNumberSet"
ParSnpSet-class Class "ParSnpSet"
plot,ParSnpCallSet,SnpCallSet-method Plots copy number and genotype calls against physical position
plot,ParSnpCopyNumberSet,SnpCopyNumberSet-method Plots copy number and genotype calls against physical position
plot,ParSnpSet,oligoSnpSet-method Plots copy number and genotype calls against physical position
plot,SnpLevelSet-method Plots copy number and genotype calls against physical position
plotCytoband Plots idiogram 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<- 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<- 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<- Accessor for graphical parameters
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