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 |
radius |
number of base-pairs in each direction to look |
chrnum |
chrnum instance .. optional |
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
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