getSnpAnnotation {SNPchip}R Documentation

Retrieves SNP-level annotation

Description

SNP-level annotation currently includes the db SNP identifier, chromosome, physical position, strand, and fragment length.

Usage

getSnpAnnotation(object, ...)

Arguments

object An object derived from eSet.
... Additional arguments

Details

Currently, this function supports only the Affymetrix 100k and 500k SNP chips. The featureNames in the eSet object must be valid Affymetrix identifiers. Two options exist for adding SNP-level annotation to an object:

1. The default method is to use the annotation packages maintained by Bioconductor. This is the preferred method as the annotation packages are continuously updated. Using the default method requires that the annotation slot in the eSet object be exactly identical to 1 of the 4 annotation packages currently provided:

a. pd.mapping50k.hind240 b. pd.mapping50k.xba240 c. pd.mapping250k.nsp d. pd.mapping250k.sty

Note that if the R package oligo was used to summarize genotype calls in the eSet object, the annotation slot is already provided.

2. Manually download the annotation provided by NetAffx and convert the file to an object of class AnnotatedDataFrame. The SNPs in the AnnotatedDataFrame must be in the same order as the SNPs in the object derivied from eSet.

Value

An object of class AnnotatedDataFrame

Author(s)

Robert Scharpf

References

See Also

oligoSnpSet, AnnotatedDataFrame, annotation

Examples


##Default method for adding SNP-level annotation
  data(sample.snpset)
## Not run: 
##Requires pd.mapping50k.xba240 annotation package
  snp.annotation <- getSnpAnnotation(sample.snpset)
  snp.annotation
  class(snp.annotation)
  identical(featureNames(obj), featureNames(snp.annotation))
  featureData(sample.snpset) <- snp.annotation
  fvarLabels(sample.snpset)
## End(Not run)

##Using NetAffx annotation (already saved as a data.frame)
## Not run: 
  
  try(load(url("http://biostat.jhsph.edu/~iruczins/publications/sm/2006.scharpf.bioinfo/mapping/mapping50kXba240.rda")))
  reorderRows <- match(featureNames(sample.snpset), as.character(mapping50kXba240$Probe.Set.ID))
  netaffx.annotation <- mapping50kXba240[reorderRows, ]
  fD <- as(netaffx.annotation, "AnnotatedDataFrame")
  featureData(sample.snpset) <- fD
  varLabels(featureData(sample.snpset))
## End(Not run)

[Package SNPchip version 1.2.1 Index]