snpsNear {GGBase} | R Documentation |
obtain list of rs numbers for snps near a gene
snpsNear(sym, radius=1e+05, chrnum, ...)
sym |
instance of genesym class [e.g., use genesym(string) for gene 'string'],
or of rsid class, or of numeric class. An instance of
GSEABase-class can also be supplied if it
has geneIdType AnnotationIdentifier. |
radius |
number of base-pairs in each direction to look |
chrnum |
chrnum instance .. optional |
... |
options not now in use |
simple arithmetic based on output of snpLocs.Hs
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
first invocation can take longer than subsequent, if snpLocs.Hs has not been invoked previously
Vince Carey <stvjc@channing.harvard.edu>
nearc = snpsNear(genesym("CPNE1"), 10000, chrnum(20)) library(GGtools) data(hmceuB36.2021) ss = smList(hmceuB36.2021)[[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("CPNE1", "ADA"), geneIdType=SymbolIdentifier()) s2 = s1 geneIdType(s2) = AnnotationIdentifier("illuminaHumanv1.db") s2 sapply(snpsNear(s2), length)