Classes and Methods for high throughput SNP chip data


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Documentation for package `SNPchip' version 1.0.0

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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.