snpsNear {GGBase}R Documentation

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

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

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

first invocation can take longer than subsequent, if snpLocs.Hs has not been invoked previously

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

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

[Package GGBase version 3.0.0 Index]