SNPperMeta-class {RSNPper}R Documentation

Class "SNPperMeta" representing data on SNPs curated at snpper.chip.org

Description

gives immediate access to location and allele, methods extract material on allele frequencies in different populations, and relationships to particular mRNAs/genes.

Objects from the Class

Objects can be created by calls of the form new("SNPperMeta", ...). The extend matrix (so that colnames are propagated).

Slots

.Data:
Object of class "matrix" see example
popDetails:
Object of class "data.frame" information on populations that have been genotyped for reference
geneDetails:
Object of class "data.frame" information on mRNAs (typically) near the SNP; putative SNP roles (in Promoter, 3' UTR, or Exon) are often denoted
submitters:
Object of class "ANY" unprocessed XML on submitter identity.

Extends

Class "matrix", from data part. Class "structure", by class "matrix". Class "array", by class "matrix". Class "vector", by class "matrix", with explicit coerce. Class "vector", by class "matrix", with explicit coerce.

Methods

popDetails, geneDetails, submitters functions are available.

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

References

snpper.chip.org

Examples

if (interactive()) {
lkc = SNPinfo("6060535")
lkc
popDetails(lkc)
geneDetails(lkc)
lkg = geneInfo("CPNE1")
lkg
dim(allGeneMeta(lkg))
 }

[Package RSNPper version 1.12.0 Index]