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)