\name{snpsNear} \alias{snpsNear} \title{ obtain list of rs numbers for snps near a gene } \description{obtain list of rs numbers for snps near a gene } \usage{ snpsNear(sym, radius=1e+05, chrnum, ...) } \arguments{ \item{sym}{ instance of genesym class [e.g., use genesym(string) for gene 'string'], or of rsid class, or of numeric class. An instance of \code{\link[GSEABase:GeneSet-class]{GeneSet-class}} can also be supplied if it has \code{geneIdType} AnnotationIdentifier.} \item{radius}{ number of base-pairs in each direction to look} \item{chrnum}{ chrnum instance .. optional} \item{\dots}{ options not now in use } } \details{ simple arithmetic based on output of snpLocs.Hs } \value{ character vector of rsxxxxxx, dbSNP id, according to locations from SNPlocs.Hsapiens.dbSNP.20071016 package, as transferred to snpLocs.Hs resource in GGBase note that an attribute 'target' is returned, a named vector with components chr and loc describing chromosome and location of the target for which nearby SNPs are sought } %\references{ } \author{Vince Carey <stvjc@channing.harvard.edu>} \note{first invocation can take longer than subsequent, if snpLocs.Hs has not been invoked previously } %\seealso{ } \examples{ nearc = snpsNear(genesym("BACH1"), 10000, chrnum(21)) data(smlSet.example) ss = smList(smlSet.example)[[1]] # following calculation requires new "[" for j an instance of rsid clo = ss[ , rsid(snpsNear(rsid("rs6060535"), rad=1500, chrnum(20))) ] clo # try a gene set library(GSEABase) s1 = GeneSet(c("BACH1", "ATP5O"), geneIdType=SymbolIdentifier()) s2 = s1 geneIdType(s2) = AnnotationIdentifier("illuminaHumanv1.db") s2 sapply(snpsNear(s2), length) } \keyword{ models }