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]