# Classes and Methods for high throughput SNP chip data

## Documentation for package `SNPchip' version 1.0.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A C D E F G H I P S U

## -- 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,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
alleleA,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
alleleA,oligoSnpSet-method | Accessor for the A allele
alleleA,SnpCallSet-class | Class "AnnotatedSnpCallSet"
alleleA,SnpCallSet-method | Accessor for the A allele
alleleA,SnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
alleleB | Accessor for the B allele
alleleB,AnnotatedDataFrame-method | Accessor for the B allele
alleleB,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
alleleB,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
alleleB,oligoSnpSet-method | Accessor for the B allele
alleleB,SnpCallSet-class | Class "AnnotatedSnpCallSet"
alleleB,SnpCallSet-method | Accessor for the B allele
alleleB,SnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
AnnotatedSnpCallSet-class | Class "AnnotatedSnpCallSet"
AnnotatedSnpCopyNumberSet-class | Class "AnnotatedSnpCopyNumberSet"
AnnotatedSnpSet-class | Class "AnnotatedSnpSet"
annSnpset | AnnotatedSnpSet object

## -- C --

centromere | Coordinates of centromere
chromosome | Accessor for chromosome SNP annotation
chromosome,AnnotatedDataFrame-method | Accessor for chromosome SNP annotation
chromosome,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
chromosome,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
chromosome,oligoSnpSet-method | Accessor for chromosome SNP annotation
chromosome,SnpCallSet-method | Accessor for chromosome SNP annotation
chromosome,SnpCopyNumberSet-method | Accessor for chromosome SNP annotation
chromosome-methods | Accessor for chromosome SNP annotation
chromosomeAnnotation | chromosome annotation
chromosomeAnnotation,AnnotatedSnpCallSet-method | Class "AnnotatedSnpCallSet"
chromosomeAnnotation,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
chromosomeAnnotation,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
chromosomeAnnotation<-,AnnotatedSnpCallSet,data.frame-method | Class "AnnotatedSnpCallSet"
chromosomeAnnotation<-,AnnotatedSnpCopyNumberSet,data.frame-method | Class "AnnotatedSnpCopyNumberSet"
chromosomeAnnotation<-,AnnotatedSnpSet,data.frame-method | Class "AnnotatedSnpSet"
chromosomeSize | Get size of chromosome in number of base pairs.
coerce,AnnotatedSnpCopyNumberSet,AnnotatedSnpSet-method | Class "AnnotatedSnpCopyNumberSet"
coerce,AnnotatedSnpSet,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpSet"
coerce,oligoSnpSet,AnnotatedSnpSet-method | Methods for Function coerce
coerce-methods | Methods for Function coerce
copyNumber,SnpQSet-method | Extracts copy number estimates
copyNumber-methods | Extracts copy number estimates
cytoband | Start and stop sites of cytoband

## -- D --

dbSnpId | The dbSNP identifier.
dbSnpId,AnnotatedDataFrame-method | The dbSNP identifier.
dbSnpId,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
dbSnpId,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
dbSnpId,oligoSnpSet-method | The dbSNP identifier.
dbSnpId,SnpCallSet-method | The dbSNP identifier.
dbSnpId,SnpCopyNumberSet-method | The dbSNP identifier.

## -- E --

enzyme | Enzyme used to digest DNA
enzyme,AnnotatedDataFrame-method | Enzyme used to digest DNA
enzyme,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
enzyme,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
enzyme,oligoSnpSet-method | Enzyme used to digest DNA
enzyme,SnpCallSet-method | Enzyme used to digest DNA
enzyme,SnpCopyNumberSet-method | Enzyme used to digest DNA

## -- F --

fData | Accessor for the data.frame in featureData
fData,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
fData,eSet-method | Accessor for the data.frame in featureData
fData<-,eSet,data.frame-method | Accessor for the data.frame in featureData
fragmentLength | Accessor for the fragment length
fragmentLength,AnnotatedDataFrame-method | Accessor for the fragment length
fragmentLength,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
fragmentLength,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"

## -- G --

getSnpAnnotation | Retrieves SNP-level annotation
getSnpAnnotation,eSet-method | Retrieves SNP-level annotation

## -- H --

hapmap | Data from the hapmap project

## -- I --

initialize,AnnotatedSnpCallSet-method | Generates instances of SnpSet objects
initialize,AnnotatedSnpCopyNumberSet-method | Generates instances of SnpSet objects
initialize,AnnotatedSnpSet-method | Generates instances of SnpSet objects
initialize,AnnotatedSnpSetList-method | Generates instances of SnpSet objects
initialize,oligoSnpSet-method | Generates instances of SnpSet objects
initialize,SnpCallSet-method | Generates instances of SnpSet objects
initialize,SnpCopyNumberSet-method | Generates instances of SnpSet objects
initialize-methods | Generates instances of SnpSet objects

## -- P --

plotCytoband | Adds cytoband to plot.
plotCytoband,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
plotSnp | Plots copy number and genotype calls.
plotSnp,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
plotSnp,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
position | Physical position of SNP on chromosome
position,AnnotatedDataFrame-method | Physical position of SNP on chromosome
position,AnnotatedSnpCopyNumberSet-method | Class "AnnotatedSnpCopyNumberSet"
position,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
position,oligoSnpSet-method | Physical position of SNP on chromosome
position,SnpCallSet-method | Physical position of SNP on chromosome
position,SnpCopyNumberSet-method | Physical position of SNP on chromosome

## -- S --

show,AnnotatedSnpSet-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,AnnotatedSnpSet-method | Class "AnnotatedSnpSet"
summary,AnnotatedSnpSet-method | Methods for Function summary
summary,ANY-method | Methods for Function summary
summary,SnpCallSet-method | Methods for Function summary
summary-methods | Methods for Function summary

## -- U --

unsplitS4 | Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet.