AnnotatedSnpSet-class {SNPchip}R Documentation

Class "AnnotatedSnpSet"

Description

Container for genotype and copy number data from SNP chips, as well as chromosome-level features

Objects from the Class

Objects can be created by calls of the form new("AnnotatedSnpSet", phenoData, assayData, experimentData, featureData, annotation, chromosomeAnnotation).

Slots

chromosomeAnnotation:
Object of class data.frame containing chromosome-level annotation
assayData:
Object of class AssayData containing copy number and genotype call matrices
phenoData:
Object of class AnnotatedDataFrame
featureData:
Object of class AnnotatedDataFrame. Contains annotation for the SNP's, such as chromosome, physical position, and alleles.
experimentData:
Object of class MIAME
annotation:
Character string for type of SNP chip. e.g., "pd.mapping50k.xba240"
.__classVersion__:
Object of class Versions

Extends

Class AnnotatedSnpCallSet, directly. Class AnnotatedSnpCopyNumberSet, directly. Class SnpCallSet, by class AnnotatedSnpCallSet, distance 2. Class eSet, by class AnnotatedSnpCallSet, distance 3. Class VersionedBiobase, by class AnnotatedSnpCallSet, distance 4. Class Versioned, by class AnnotatedSnpCallSet, distance 5. Class SnpCopyNumberSet, by class AnnotatedSnpCopyNumberSet, distance 2. Class eSet, by class AnnotatedSnpCopyNumberSet, distance 3. Class VersionedBiobase, by class AnnotatedSnpCopyNumberSet, distance 4. Class Versioned, by class AnnotatedSnpCopyNumberSet, distance 5.

Methods

alleleA
signature(object="AnnotatedSnpSet"): return the A allele for the specified SNPs in object
alleleB
signature(object="AnnotatedSnpSet"): return the B allele for the specified SNPs in object
chromosome
signature(object="AnnotatedSnpSet"): accessor for the chromosome
fData
signature(object="AnnotatedSnpSet"): accessor for the data.frame containing feature-level annotation. Usually very large.

fragmentLength
signature(object="AnnotatedSnpSet"): accessor for the length of the PCR fragment on which the SNP resides

plotCytoband
signature(object="AnnotatedSnpSet"): Plots the cytoband for a single chromosome.
plotSnp
signature(object="AnnotatedSnpSet", ...): Makes a scatterplot of copy number (vertical axis) versus physical position (horizontal axis) for each chromosome and sample in the AnnotatedSnpSet object. Points are color-coded by the genotype call.
position
signature(object="AnnotatedSnpSet"): Returns physical position of SNP along the chromosome in numbers of basepairs from the 5' end (an integer)

Note

Author(s)

Rob Scharpf

References

See Also

plotSnp

Examples

data(annSnpset)
annSnpset
##for formatting the plot layout, see the vignette
plotSnp(annSnpset, 1:10, 1:2)

[Package SNPchip version 1.0.0 Index]