# Classes and Methods for high throughput SNP chip data

## Documentation for package ‘SNPchip’ version 1.16.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

$-method | Class "ParESet"
$<--method | Class "ParESet"
addFeatureData | Method for Function addFeatureData
addFeatureData-method | Method for Function addFeatureData
addFeatureData-methods | Method for Function addFeatureData
alleleA | Accessor for the A allele
alleleA-method | Accessor for the A allele
alleleB | Accessor for the B allele
alleleB-method | Accessor for the B allele
centromere | Coordinates of centromere
chromosome | Accessors for feature-level SNP annotation
chromosome-method | Accessors for feature-level SNP annotation
chromosome-methods | Accessors for feature-level SNP annotation
chromosomeAnnotation | chromosome annotation
chromosomeSize | Size of chromosome in number of base pairs.
coerce-method | Methods for Function coerce
coerce-methods | Methods for Function coerce
crlmmOut | A data object created by the oligo vignette
cytoband | Start and stop sites of cytoband
dbSnpId | The dbSNP identifier
dbSnpId-method | The dbSNP identifier
enzyme | Enzyme used to digest DNA
enzyme-method | Enzyme used to digest DNA
fragmentLength | Accessor for the fragment length
fragmentLength-method | Accessor for the fragment length
getPar | Adds graphical parameters for plotting SNP data
getPar-method | Adds graphical parameters for plotting SNP data
hapmap | Data from the hapmap project
hmmPredict | Accessor for HMM output
hmmPredict-method | Class "ParESet"
initialize-method | Class "ParESet"
initialize-method | Class "ParSnpCallSet"
initialize-method | Class "ParSnpCopyNumberSet"
initialize-method | Class "ParSnpSet"
integer2chromosome | Converts integer representation of chromosome number back to letter representation
ParESet-class | Class "ParESet"
ParSnpCallSet-class | Class "ParSnpCallSet"
ParSnpCopyNumberSet-class | Class "ParSnpCopyNumberSet"
ParSnpSet-class | Class "ParSnpSet"
plot | Plots copy number and genotype calls against physical position
plot-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-method | Class "ParESet"
plotSnp-method | Plots copy number and genotype calls against physical position
position | Accessors for feature-level SNP annotation
position-method | Accessors for feature-level SNP annotation
position-methods | Accessors for feature-level SNP annotation
sample.snpset | Example object of class oligoSnpSet
show-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-method | A simple nonparametric smoother for genotype and copy number
snpPar | Accessor for graphical parameters
snpPar-method | Class "ParESet"
snpPar<- | Accessor for graphical parameters
snpPar<--method | Class "ParESet"
snpset | Accessor for SNP data
snpset-method | Class "ParESet"
summary-method | Summary statistics for various SNP classes that extend eSet
summary-methods | Summary statistics for various SNP classes that extend eSet
updateObject-method | updateObject methods