# Classes and Methods for high throughput SNP chip data

## Documentation for package ‘SNPchip’ version 1.8.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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,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