| getSnpAnnotation {SNPchip} | R Documentation |
SNP-level annotation currently includes the db SNP identifier, chromosome, physical position, strand, and fragment length.
getSnpAnnotation(object, ...)
object |
An object derived from eSet. |
... |
Additional arguments |
Currently, this function supports only 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.
An object of class AnnotatedDataFrame
Robert Scharpf
oligoSnpSet,
AnnotatedDataFrame,
annotation
##Default method for adding SNP-level annotation
data(annSnpset)
obj <- new("AnnotatedSnpCopyNumberSet",
copyNumber=copyNumber(annSnpset)[1:50,],
cnConfidence=cnConfidence(annSnpset)[1:50,],
phenoData=phenoData(annSnpset), annotation=annotation(annSnpset))
obj
## Not run:
##Requires pd.mapping50k.xba240 annotation package
snp.annotation <- getSnpAnnotation(obj)
snp.annotation
class(snp.annotation)
identical(featureNames(obj), featureNames(snp.annotation))
featureData(obj) <- snp.annotation
validObject(obj)
varLabels(featureData(obj))
## 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(obj), as.character(mapping50kXba240$Probe.Set.ID))
netaffx.annotation <- mapping50kXba240[reorderRows, ]
fD <- as(netaffx.annotation, "AnnotatedDataFrame")
featureData(obj) <- fD
varLabels(featureData(obj))
validObject(obj)
## End(Not run)