| AnnotatedSnpSet-class {SNPchip} | R Documentation |
Container for genotype and copy number data from SNP chips, as well as chromosome-level features
Objects can be created by calls of the form new("AnnotatedSnpSet", phenoData, assayData, experimentData, featureData, annotation, chromosomeAnnotation).
chromosomeAnnotation:data.frame containing chromosome-level annotation assayData:AssayData
containing copy number and genotype call matrices phenoData:AnnotatedDataFrame featureData:AnnotatedDataFrame. Contains annotation for the SNP's,
such as chromosome, physical position, and alleles. experimentData:MIAME annotation:.__classVersion__:Versions
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.
signature(object="AnnotatedSnpSet"): return
the A allele for the specified SNPs in objectsignature(object="AnnotatedSnpSet"): return
the B allele for the specified SNPs in objectsignature(object="AnnotatedSnpSet"):
accessor for the chromosomesignature(object="AnnotatedSnpSet"):
accessor for the data.frame containing feature-level annotation.
Usually very large.signature(object="AnnotatedSnpSet"):
accessor for the length of the PCR fragment on which the SNP residessignature(object="AnnotatedSnpSet"):
Plots the cytoband for a single chromosome.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.signature(object="AnnotatedSnpSet"): Returns
physical position of SNP along the chromosome in numbers of
basepairs from the 5' end (an integer)Rob Scharpf
data(annSnpset) annSnpset ##for formatting the plot layout, see the vignette plotSnp(annSnpset, 1:10, 1:2)