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]